The Hammers were last week accused of sex discrimination by Stephen Hunt, chairman of the ladies' club.
West Ham said they will now work in unison with the ladies' team to ensure key improvements are made.
Vice-chairman Karren Brady said the Premier League club are "passionately committed to equality".
She added women's football was a "high priority on our agenda".
Hunt had told BBC Sport West Ham should "start to act like a 21st century club" and claimed they had stopped his team from finding sponsors, adding the ladies were short on funds because they had to buy their own kit.
In response, West Ham claimed Hunt had "refused to align" with their principles.
The ladies' team, who this season celebrate their 25th anniversary, play in the FA Women's Premier League Southern Division.
Brady added: "The addition of the ladies into the West Ham family is the solution my board and I have long sought.
"Not only does it secure the long-term future of the ladies' side, but also guarantees current and future supporters, players and staff of the ladies' team will form an integral part of the club's bright future as we move forward."
As part of the agreement, the West Ham Ladies' Academy will also be managed by the Premier League club.

The Gills, who finished 20th in League One last season, have signed eight players so far this summer.
But having started the season with a 0-0 draw to Doncaster and a 2-0 loss to Reading, Pennock wants more recruits.
"They've got to be the right players, the right characters and more importantly they've got to be good players," Pennock, 46, said.
"Everybody is pulling together in the right direction - it's a good changing room and if we can add two or three more I'll be very happy."
Although the club are still on the lookout for new additions, Pennock is pleased with those who have already arrived.
Gillingham have brought in defenders Gabriel Zakuani, Luke O'Neill, Connor Ogilvie and Alex Lacey, strikers Liam Nash, Conor Wilkinson and Tom Eaves and midfielder Billy Bingham.
"Overall, I'm happy with every single one of them - all of the new lads who have come in have contributed to what we've done, they've been absolutely first-class," Pennock told BBC Radio Kent.
"I think it's pushed the others on who were here last year as well. The whole club at the moment is in a good place."

It comes after Denbighshire council was granted permission to compulsorily purchase the former North Wales Hospital in Denbigh.
Owner Freemont (Denbigh) Ltd had opposed the compulsory purchase.
There has been a long-running dispute between both sides concerned about the future of the historical building.
The Rightmove website advert said the council "does not intend to develop the site but to work with a third party/developer that will".
The council had agreed to pass ownership of the building to the North Wales Building Preservation Trust, a non profit-making organisation which will receive support from the Princes Regeneration Trust.
The property is set for auction later this month.
A Denbighshire council spokesperson said the owners had the right to try to sell it as the hospital site has still not been transferred into the ownership of the council.
He said the authority would still continue with the compulsory purchase process.
"The High Court's ruling in March means that we are one step closer to handing over the site to the trust.
"However, there are many issues to be resolved before the council can take ownership and for the council to pass the ownership on to the trust.
"If the site is sold in the meantime, the council would need to negotiate with the new owner."
West Ham United have taken over the running of the ladies' club, saying they are "delighted" to bring it into "the West Ham family".
[NEXT_CONCEPT]
Gillingham are looking to add "two or three" more players to their squad, according to manager Ady Pennock.
[NEXT_CONCEPT]
The owners of a former Victorian asylum in north Wales have put it on the market for potential redevelopment with a £2.25m price tag.