The WSFF's logo will appear on the team's training kit as City makes its debut in the FA Women's Super League.
It is the first non-commercial partnership to be announced since the Premier League club announced the formation of its women's team.
Founded in 1984, the WSFF is a UK charity focused on increasing female participation and involvement.
“This partnership with MCWFC is the first time we have officially collaborated with a football team and we are delighted that one of the biggest clubs in world sport is demonstrating such a strong commitment to the women’s game.
"Our shared values will help create a strong pathway to get women more involved in sport.”
Tom Glick, the managing director of City Football Marketing, added: “As we enter our very first season in the FA Women’s Super League it’s important to us that we have the right partners on board. We hope that this unique partnership will have a real and lasting impact on girls’ and women’s sport both in the UK and worldwide.
“The players are fantastic role models to young people and we, with the WSFF, are fortunate to have a platform to showcase that to the next generation of sportswomen.”
City's first Super League game is scheduled for Thursday evening, at Liverpool Ladies. The club will play its home games at Manchester's Regional Athletics Arena this season, before it moves into the newly-constructed 7,000 capacity City Football Academy in 2015.