The first Headmaster was Mr.Cox, who also happened to be the owner and manager of a printing press. Most of the headmasters who succeeded him thereafter were either of previous service in the Government or military. Right until 1853, the school saw the service of 7 Headmasters, none of whom were really trained or qualified to head a school. 

In 1853, the Committee decided to engage an elementary schoolmaster from England as Headmaster. Hitherto the education given was only elementary in character. To raise the standard of education in the school, the Committee decided upon the appointment of a University graduate as Headmaster. The first such Headmaster was Mr. W. Hargreaves who assumed the post in 1891.

 The Free School remains greatly indebted to Mr. W. Hargraves for his conscientiousness and dedication which instilled new life and vigour into it, projecting it forward as the foremost educational institution in the Colony. During his term of office (1891 — 1904), the school noted tremendous scholastic achievements unparalleled by any other institution in the region.

Under the guidance of Mr. Hargreaves, there was an increase in enrolment. The former system of mixing up different age groups within a class was abolished. The increase in enrolment also brought about a need for

money. An endowment fund was started but this only solved financial problems temporarily. In 1903 the school was again in need of money. In response to the recommendation of the Kynnersley Committee of 1902, the Government decided to intervene and take over the administration of the school. However as a result of local protest, the committee of Directors rejected the offer and instead accepted an annual grant in addition to the usual grant-in-aid.

Under his tenure, ten students won the “Queen’s Scholarship.” The first student who received the award was Mr. Ung Bok Hoay (1893), followed by Mr. Gnoh Lean Tuck (1896) also known as Dr. Wu Lien Teh. Our former Chief Minister of Penang, Dr. Lim Chong Eu was also a recipient of that prestigious award (1937)

From 1905 to 1925, the school saw the service of Mr. R.H.Pinhorn as Headmaster. Mr. Pinhorn was responsible for the implementation of regular and systematic games and extra-curricular activities for all students. The aim of this vigorous programme of extra-mural activities was the development of qualities of initiative, responsibility and leadership.

By the 1920s, the school was badly over crowded and to accommodate the rising enrolment, the government acquired a new site of 30 acres in Green Lane.

Construction of the new buildings commenced in 1924 and on the 9th of January, the new school buildings in Green Lane were officially declared open by the Resident Councilor of Penang, Mr. Ralph Scott. The old building was renamed 'Hutching's School' catering  for primary education while Penang Free School became a secondary institution. The old building is now the State Museum. W.Hamilton was the principal then 1925 to 1926. He was succeeded by Mr. D.R.Swaine (1927 — 1928) and following the shifting to the school to its new buildings, he implemented radical changes in the extra-curricular activities. A new experiment was launched whereby the House System came into existence. There were initially only five Houses and these Houses governed activities like Scouting and games.

The administration of the school was initially the responsibility of a Committee of Directors. However, on the first of January 1920, by the passing of the Penang Free School (Acquisition) Bill, the Government took over the management of the school. The school, however, retained its endowments, administered by a Board of Trustees and chaired by the Chief Minister of Penang. The trustees are responsible for the provisions of scholarships for deserving students. One such scholarship is the Hutchings scholarship. In 1928,L.W. Arnold took over the leadership and guided the school for a year 1928 to 1929 and the headmaster's ship was handed over to D.W. Mc Leod (1929 to 1931)

Under the Headmastership of Mr. M.Holgate (1931 — 1933) the present system of awarding school prizes came into existence. Expansion in sports gave rise to games like volleyball, basketball and rugby football. The school swimming section was formed in March

1936 and the Additional sports System was started to enable all boys to develop the feeling of loyalty to the House. A school rule was established whereby every boy was to participate in some form of extra-mural activity. Having much love for the school L.W. Arnold came back to champion for the school from 1934 to 1946 but had to leave because of the second world war. When L. W Arnold left D. Roper took over from 1947 to 1950. D.Roper was succeeded by P.F. Howitt (1950 to 1951). The school was hard to manage then as many precious documents were destroyed during the war.

With the implementation of the Educational Ordinance in 1957, Penang Free School became a national-type fully assisted secondary school run by a properly constituted Board of Governors. Since the loss of "Government" status, the provision of more facilities for the school had been greatly affected.

Mr. J.E.Todd (1951 — 1957) was largely responsible for Sixth Form education as it exists today and he also worked along the principles of Mr. Pinhorn in extra-mural activities. Between 1957 and 1965 there was an even greater expansion of clubs and societies.

Mr. Todd was championed by J.M.B Hughes in 1957. The late YTM Tunku Abdul Rahman Putra Al-Haj officially declared open the Sixth Form block and Hostel on 21st October 1958. Free School then became the centre of Sixth Form education in Northern Malaya.1966 was undoubtedly a very important year for the school as it held its Sequicentenary Celebrations.

In 1963, Mr. Tan Boon Lin (1963 to 1968) became the School’s first Asian Headmaster. During his tenure of office the School’s new library, the Khutub Khanah Tunku was added.

The Penang Free School Development Fund was launched in early 1963. The objective of this fund was to raise money for a number of building projects including a swimming pool. A Food and Fun Fair held in April 1963 netted a collection of RM18,622. However, the 'Swimming Pool Project' was shelved and in its place, a new library was planned.

It became a reality on 29th of December 1969, when the first Prime Minister of Malaysia, the late Tunku Abdul Rahman Putra Al-Haj who was an old Free, officially opened it. The library was named “Kutub Khanah Tunku” to honour him. Our late Prime Minister of Malaysia donated $100,000.00 for this project. In December 1990, he made his last visit to his Alma Mater in conjunction with the Library's 20th Anniversary.

Under the Headmastership of Mr. Poon Poh Kong (1969 — 1971) the school had another Fun Fair and a Raffle. The proceeds amounts to $30,000 and $53,000 respectively went to the School Develompent Fund.

When Mr. K.G.Yogam (1972 — 1974) took over as Headmaster, the Nuffield Science block, the Industrial Art Workshop and the present Hostel were built. With the completion of the new

hostels, the old hostels on the second floor of the Sixth Form block was converted into classrooms and now forms part of the present Sixth Form Block.

             In 1975, when Mr. Goon Fatt Chee was Headmaster, the school enrolment passed the 2000 mark for the first time in history. The strength of the teaching staff was 87. This reflects the tremendous development of the school in terms of students and teacher population.

Under his leadership, with the help of the Choong Family, Mr. Choon Beng and Mr. Lim Hock Seng, the school arch was erected in 1977. The school arch was officiated by Dato’ Ch’ng Eng Hye on the 21st October 1978. In 1977, the second hostel together with the school pond came into existence.

 Mr. R. Visvanathan took over the Headmastership in 1980 under his leadership, Block B of the school was completed. The population of the school hostel rose to 334 students. In 1983, Mr. G Krishna Iyer lead the school and under Mr. G Krishna Iyer the school was completely rewired at a cost $92, 000 and the students’ washroom were renovated in 1987.

In 1988, the Form One students were on the threshold of the new academic era with the implementation of KBSM (Integrated Curriculum for Secondary Schools). The following year saw the teaching of a new subject "Kemahiran Hidup" (Living Skills) to the First Formers.

It is also in that very year the Headmastership was taken over by Mr. Goh Hooi Beng. Mr. Goh Hooi Beng was assisted by Mr. Loo Hock Guan. Under his tenure Penang Free School adopted the single session school system with the construction of two new blocks

Mr. Goh was succeeded by Haji Mohd Ismail B. Ibramsa in 1994. Under Haji leadership the school resource centre was greatly improved and the side gate at Free School Road was constructed and financed by Mr. C.A.Goh, an old Free and troop leader of the 7th Georgetown Scout Troop.

The following year saw the introduction of compulsory IT education for all Form 1 students who have to continue their computer classes until Form 3, a move in line with the national education policy to produce computer literates. The school computer club then was Mr. Kong Fun Chong. Under Mr. Kong, Penang Free School became the first school in Malaysia to linked to the outside world through internet and it is the first school that has its own proper website.

The school computer club was then taken over by Mr. Ooi Chin Wah in 1998. Mr. Ooi was the teacher advisor that leads the school computer club to its peak. He is also the webmaster who redesigned the school website as what is it today. In 1998, a new block (H) was added just by the side of the school canteen. The new block has a modern meeting room, a multimedia resource centre and class rooms. The first multimedia resource centre was coordinated by Mr. Ch’ng Yeang Soon who with the help of the Parent Teachers’ Association (PTA, 2000/2001) has donated 20 Pentium 3 multimedia computers to the school. The computers are still in use till today.

Penang Free School Foundation was officially registered with the Registrar of Society on 19th April 1996. It was launched officially by the Deputy Prime Minister YAB Datuk Seri Anwar Ibrahim on 15th September 1996. The primary aim of the Foundation is to help the school to achieve greater heights in education and at the same time to preserve the rich traditions and glories of Penang Free School.

From March 1999 onwards, work on the upgrading of the school, as a premier school commenced and scheduled to be completed in August. Within this year itself, two new blocks are constructed to meet the ever-demanding needs of the school.

In 2000, Mr. Abdul Rahman B. Haji Salim lead the school for only a very short term. He was succeeded by Mr. Arabi B. Sulaiman in August 2001. Under Mr. Arabi, the school ICT infrastructure was further improved. Mr. Arabi retired in this school on July 2004. The Headmastership was temporary shouldered by Mr. Khoo Poh Kheng who later in 2005 became the Headmaster of Hutching Secondary School.

In 2003, the teachers from the school was awarded the “Master Teacher title” They are Mr. Ch’ng Yeang Soon, Master Teacher for Additional Mathematics and Mr. Ooi Eng Lye a Master Teacher for General Studies. Penang Free School is one of the very few school that has two Master Teachers.

Haji Mohammad Yusof B. Omar was appointed the following year after Mr. Arabi retired. Haji Mohammad Yusof, was assisted by Mr. Loh Huah Sin and Ms. Yew  Lee Heang took over Mr. Loh’s post as the head of Science and Mathematics.

In 2006, Haji Ramli B. Din was appointed the new headmaster of Penang Free School. Under his leadership, many changes took place.

Haji Ramli introduces two new foreign languages, namely French and Arabic language. At the moment, the two languages will only be taught to the lower secondary students and if it is successful it will then be introduce to the upper secondary.

The school is providing wireless connection for the school so that her students as well as teachers may access the internet anyway within the school compound. This brave step is essential to enable the citizen of the school to communicate and access useful information using the internet and enhancing the teaching and learning process.

Being far sighted, Haji Ramli appointed Mr. Goh Teng Keang to assist him after Mr. Loh has retired. Haji Ramli’s has invited his teachers to work together with him to propel Penang Free School to greater height. The synergizes worked! On 30th March 2007 a year after his appointment as headmaster, the school was given the “Cluster School of Excellence Award” This is indeed a very big achievement as only 30 schools are awarded this status as pioneers under the Ninth Malaysian Plans.

A group of these Headmasters under the Cluster School Status will be sent to attend a few months course in Australia. Under Haji Ramli’s tenure, more infrastructures were erected, shaded car park was erected for the teachers, rain shades were erected for the students and parents so that their children wont get wet during rainy days. Haji Ramli Bin Din is a very conscientious and dedicated headmaster. The teachers under his watchful eyes worked very hard and he insisted to meet with the teachers every Wednesday after school for a brief discussion concerning the school vision, mission and to put forwards his ideas for the betterment of the school.

The school has two assemblies. Monday assembly is for Academics and purposes while Wednesdays assembly is mainly for Co-curriculum. Mr. Goh Teng Keang who was later succeeded by Mr. Ho Nean Chan as the new senior assistant of administration; an old Frees in 2008.