Mendonca started his career with Sheffield United, before spells with Doncaster Rovers, Rotherham United and Sheffield United again. Mendonca then moved to Grimsby Town in 1992, initially on loan. Mendonca scored 60 goals in 166 appearances for Grimsby, and is considered to be their best striker in recent history. Mendonca moved to Charlton Athletic in the summer of 1997 and scored twenty eight times for the Addicks in the 1997–98 season, including a hat-trick against his home town team Sunderland who he'd supported as a boy, in the Division One play-off final at Wembley. His hat-trick in 1998 was the last one to be scored at the original Wembley Stadium for an English league team. Mendonca also scored a penalty in the subsequent penalty shoot-out after a 4–4 draw, which Charlton won 7–6.