A general meeting for Friends in the Delaware Valley area was first convened at Burlington in 1681. The first general meeting held in Philadelphia was in 1683, and in 1685, it was agreed that the meetings in New Jersey and Pennsylvania should be combined into one yearly meeting with alternate sessions at Philadelphia and at Burlington. Since 1760, all Philadelphia Yearly Meetings have been held at Philadelphia.

The are of the Yearly Meeting has diminished over time. Generally its territory now embraces eastern Pennsylvania, southern New Jersey, Delaware, and the eastern shore of Maryland. in 1790, Warrington Quarterly Meeting and Fairfax Quarterly Meeting were transferred to Baltimore Yearly Meeting in exchange for the old meetings on the Eastern Shore of Maryland, which formed Southern Quarterly Meeting. In 1819, several components of Western Quarterly Meeting were similarly transferred.

The great Separation among Philadelphia Friends occurred at the Yearly Meeting of 1827. From that year, there were two official Philadelphia Yearly Meetings, one of the Hicksite, the other of the Orthodox branch. Both were located in Philadelphia. Orthodox Friends retained possession of the meeting house on Arch Street and are often referred to as "Arch Street" Friends. The Hicksites are often referred to as "Race Street" Friends since their Yearly Meeting was held at a meeting house, built in 1857, on Race Street.

The two Yearly Meetings remained similar in structure, although the Orthodox Friends were fewer in number. There were some distinctions. Southern Quarterly Meeting was discontinued by the Orthodox in 1828; it continued with the Hicksites and evolved into the present Southern Half-Yearly Meeting. The Hicksite meetings in northern New Jersey were transferred to New York Yearly Meeting in 1833, while the Orthodox meetings in this area were retained by PYM. Several monthly meetings, including Muncy and Roaring Creek, in the central part of Pennsylvania, formed Fishing Creek Half-Yearly Meeting of PYM (Hicksite) in 1834; the Orthodox counterparts of these meetings retained part of Philadelphia Quarterly Meeting. The discontinuance of several Orthodox monthly meetings in New Jersey led to the formation of the combined Burlington and Bucks Quarterly Meeting in 1898 and Haddonfield and Salem Quarterly Meeting in 1904. The comparable Hicksite quarters did not merge.

Through the course of the early 20th century, the PYMs began to draw back together. Many standing yearly meeting committees, such as the Committee on Race Relations, Young Friends Movement, and Friends Peace Committee, perceiving concerns common to both branches of Friends, began to report to or receive appointments from both Yearly Meetings. As early as 1937, the two Yearly Meetings began to hold occasional business sessions together. In 1946, a new organization, Philadelphia General Meeting, composed of all members of the two Yearly Meetings, was formed to express the growing unity of the two Yearly Meetings. Its last session was held in 1954, but it was not until the next year that organic union was formally approved, and a reunited PYM, the present organization, was created.