The origins of Port Seton lie a little inland at the tiny hamlet of Seton, where Seton Palace was built by the Seton family. Robert Seton, 1st Earl of Winton began the initial  harbour construction and his 2nd son, George, 3rd Earl of Winton continued and finished it in 1656. It was used primarily as a fishing harbour, though it also serviced the Seton estate.  The Setons backed the Jacobite causes in the 1689, 1708, and 1715 uprisings and their estates in the area were forfeited as a result. The York Buildings Company, which took over management of the estate's mining interests, built the Tranent Waggonway in 1722. This was a horse-drawn railway carrying coal from the pits of Tranent to the Cockenzie harbour.

The 1745 Jacobite uprising the Battle of Prestonpans took place a mile south of Cockenzie and close to the line of the waggonway. History was made when the waggonway was used to transport troops to the battle, marking the railway's first ever use in warfare. Cockenzie was also home for many years to boatyards producing fishing vessels and yachts. The sheds and slipways remain, but the last vessel was produced in the mid 1990s. Fishing remains important to the whole community. This is obvious from the harbours, unusual along this coast in being home to more working vessels than pleasure craft. The importance of fishing is also obvious from the continuing presence of traditional fish merchants and curers in the village.

One of the more obvious recent developments took place in the 1960s when the Cockenzie Power Station was built on the coastal site of a disused coal mine just to the west of Cockenzie and Port Seton. The site was chosen to make use of the excellent coal supplies available locally, the good rail links, and the availability of seawater for cooling: hence the absence of cooling towers. But though the power station dominates westward views from the village, there are less attractive neighbours you could have. And and the continuing presence of the power station has probably helped protect the communities here from being swamped by their proximity of Edinburgh, only a dozen miles to the west. As a result the village retains the sense of a living and working place rather than a dormitory. In many ways Cockenzie and Port Seton feels much more like the sort of fishing villages found on the coast of Aberdeenshire or Moray than somewhere right on the doorstep of Scotland's booming capital.