Born in Randwick to farmer Magnus Jackson Peden, a mayor of Randwick, and Elizabeth Neathway Brown, he attended public school at Bega before studying at Sydney Grammar School and the University of Sydney, where he received a Bachelor of Arts in 1892 and a Bachelor of Laws in 1898.

[1] Upon leaving secondary school, Peden matriculated in 1889 to the University of Sydney, from where he graduated with a Bachelor of Arts in 1892 with first-class honours in Latin and in logic and mental philosophy.

On 4 August 1898, was called to the Bar of New South Wales and worked in the chambers of Sydney barrister Richard Meares Sly.

[3] In 1913 Peden was appointed a commissioner in the Royal Commission of inquiry into the possibilities of the establishment of a Greater Sydney Council, with the final report expressing that: Sydney is a magnificent site for a city, but the built upon area has many serious defects for want of co-ordinative town planning, and the way to safeguard against similar defects in its future expansion is to have a comprehensive and careful lay-out of the metropolitan area as soon as possible.

Its urgency is a strong reason, both for a Greater Sydney being brought to existence and for the new body giving its immediate and earnest attention.

[1] Serving as chairman of the professorial board in 1925–1933, Peden was due to retire in April 1941, but offered to volunteer his services for the duration of the war.

On 6 May 1917 Peden was given a life appointment to the New South Wales Legislative Council by Governor Sir Gerald Strickland on the advice of Premier William Holman, taking up his seat as a Nationalist on 17 July 1917.

He drafted section 7A of the Constitution Act of 1902, added by amendment in 1929, to ensure that the council could not be abolished, nor its powers be altered, except through the expression of the people through a referendum.

Lang had requested Governor Sir Philip Game and his predecessor, De Chair, for sufficient appointments to the Legislative Council in order to pass these bills, but on each occasion was met with refusal.

The following day, two members of the Legislative Council, Thomas Playfair and Arthur Trethowan, applied for and were granted an injunction preventing Lang and his ministers from presenting the bills to the Governor without having held a referendum.

On 23 December the Supreme Court of New South Wales in the case of Trethowan v Peden, upheld the injunction and ordered the government not to present bills to abolish the council for royal assent, unless ratified by the electors in a referendum.

Peden was cremated at Northern Suburbs Crematorium after a service at St Andrew's Cathedral, with an address from Bishop of Newcastle, De Witt Batty: "Sir John could be classed among the great, not only for the high positions he had held and the fund of his knowledge, but for the splendour of his personal character, [...] Sir John's name would always be associated, too,'with the movement for the spiritual autonomy of the Anglican Church in Australia.