João Manuel Perera Junqueira (born 24 June 1965 in Chaves, Alto Trás-os-Montes) is a retired Portuguese runner who specialized in the 3000 metres steeplechase.
He competed in his special event at the 1991, 1993 and 1999 World Championships and sixth-placed in 10,000 m in 1994 European Athletics Championships as well as the 1992 Summer Olympics.
At the 1993 World Cross Country Championships he earned the distinction of a bronze medal in the team competition, having finished 41st in the individual long race.
He then recorded his best placing with a 23rd place in the 1998 short race, the team finishing fifth.
He was also a part of the sixth-placed Portuguese team at the 2001 World Cross Country Championships.