Its source is near Simuna on the southern slopes of the Pandivere Upland.

The river flows for 122 km through Lääne-Viru, Jõgeva and Tartu counties before joining the Emajõgi northeast of Lake Võrtsjärv.

The last 4 km section of the river after confluence with Põltsamaa is known as the Pede.

The Pedja is also the origin of the name of Alam-Pedja Nature Reserve, a large protected area on the river's lower reaches.

This article related to a river in Estonia is a stub.