The Alconbury Brook rises in three streams in Northamptonshire which unite near Thurning, Northamptonshire and flow eastwards to Luddington in the Brook and into Huntingdonshire, where it expends the rest of its course.
After half a mile marking as the county border, the Alconbury Brook comes to Chapel End, Great Gidding and wanders down south-eastwards to Hamerton. It follows a winding course down to Alconbury Weston and then to Alconbury, the first substantial village on the brook.
From Alconbury, the Alconbury Brook passes under the A1(M) and flows generally southwards, skirting around Huntingdon Racecourse and by Brampton where it broadens amongst the meadows. It crosses under the A14 and by the edge of the county town, Huntingdon by Hinchingbrooke and falls into one of the two branches of the Great Ouse which pass around the great meadow of Port Holme.