The former England international was the first male English football professional to come out openly as gay in 1990 and died of suicide in 1998.
Fashanu was the first black footballer to command a £1m transfer fee with his move from Norwich City to Nottingham Forest in 1981. He played for a total of 22 clubs in England, North America, Scotland and New Zealand.
His niece Amal Fashanu, who campaigns against homophobia in sport and co-founder of The Justin Fashanu Foundation, received the award on his behalf. She said: "Today would have been Uncle Justin's 59th birthday and what a way to celebrate it on his behalf.
Fashanu's induction coincided with the launch of the National Football Museum's LGBT+ Tour which features objects from the museum's collection, telling the story of LGBT+ history within the context of football.
National Football Museum chief executive Tim Desmond added: "We're delighted to present this award to Amal Fashanu on behalf of Justin and the Justin Fashanu Foundation.
"The National Football Museum Hall of Fame aims to recognise a wide diversity of individuals who've made an outstanding contribution to the game.