The settlement has existed as a fishing village since early medieval times. The oldest structure, St. Fillan's Cave, dates from the 7th century. An Augustinian priory moved here from the Isle of May in the 13th century, but there was already a church at that time. Pittenweem Parish Church (which is attached to the local tolbooth) has a Norman doorway dating to before 1200. The gatehouse to the east is 15th century. The priory dormitory and refectory was remodelled post-Reformation (1588) to give a new function as a manse. This building was later named the "Great House".[1]

Until 1975 Pittenweem was a royal burgh, having been awarded the status by King James V (1513–42) in 1541.[2]

Founded as a fishing village around a probably early Christian religious settlement, it grew along the shoreline from the west where the sheltered beaches were safe places for fishermen to draw their boats up out of the water. Later a breakwater was built, extending out from one of the rocky skerries that jut out south-west into the Firth of Forth like fingers. This allowed boats to rest at anchor rather than being beached, enabling larger vessels to use the port. A new breakwater further to the east was developed over the years into a deep, safe harbour.[3]

 Cove Wynd – a typical alley in Pittenweem

In 1779 John Paul Jones (founder of the American Navy) anchored half-a-mile off Pittenweem in the USS Bonhomme Richard.[4]

There is a feudal Lordship and Barony of Pittenweem created by James VI for Frederick Stewart in 1609. It was held by the Earls of Kellie until it passed to Sir John Anstruther and then to the Bairds of Elie. The current Lord Baron is Claes Zangenberg.[5]