Rising as the Cogtail Burn in the Garleton Hills, a mile (1.5 km) north of Haddington in East Lothian, the Peffer Burn flows for 8 miles (13 km) in a northeasterly direction to empty into the North Sea at Pefferside, 1¼ miles (2 km) northwest of St Baldred's Cradle and 4 miles (7 km) northwest of Dunbar.
Another Peffer Burn flows westwards 2 miles (3 km) to the north.