The club released a statement on Wednesday detailing the initiative that will see them take on LGBTIQ issues within both football while investigating ways to best integrate inclusion and equality in football.
The partnership sees them join 'Team Pride', a coalition of international organisations who are working to promote equality for LGBTIQ players and fans in sport, with VIsa and Adidas among the participants.
Taking part in the charity's Rainbow Laces campaign last year, United will now host Stonewall's Rainbow Laces Summit later in the year in an event with meetings designed to implement more inclusive policies.
Chief Executive of Stonewall Ruth Hunt highlighted the impact having the support of such a big club could have for improving equality.
"Manchester United’s support means we can reach millions of football fans both here and around the world, to encourage them to do their part in making all people feel welcome in sport," Hunt said.
"It’s crucial for organisations like Manchester United to show they not only welcome LGBT people, but are active in leading the change. At the moment, many LGBT people want to take part in sport, either as players or fans, but the behaviour of a minority can make them feel unsafe, unwelcome or unable to be themselves.
United's Managing Director Richard Arnold emphasised the honour the club felt in breaking new ground.
"Manchester United always looks to be a leader in everything it does and we are proud to be the first sports club to sign up to Team Pride," Arnold said.
"The club has an ongoing commitment to equality across all areas and with 659 million followers around the world, it is our responsibility to show support and recognition to everybody who loves this football club.
"We have built up a positive working relationship with Stonewall and it’s a great way for us to learn from each other and progress together as we strive for equality for all of our supporters.