The 1988–89 Associate Members' Cup was the eight staging of a secondary football league tournament, and the sixth staging of the Associate Members' Cup, a knock-out competition for English football clubs in the Third Division and the Fourth Division. The winners were Bolton Wanderers and the runners-up were Torquay United.
Preliminary round
Northern Section Southern Section ==First round==
First round
Northern Section Southern Section ==Quarter-finals==
Quarter-finals
Northern Section Southern Section ==Area semi-finals==
Area semi-finals
Northern Section Southern Section ==Area finals==
Area finals
Northern Area final {{football box {{football box Southern Area final {{football box {{football box ==Final==