Žeimena begins in Labanoras Forest and at Lake Žeimenys.

Its confluence with Neris is located near the border of Švenčionys and Vilnius districts.

The main tributaries of Žeimena are Lakaja, Saria, Mera [lt], Kiauna, Luknelė and Jusinė.

The length of Žeimena is an object of discussion because it originates in a large lakeland of Aukštaitija National Park.

Traditionally, Lake Žeimenys is considered to be the source of Žeimena.