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The 21-year-old, who is the son of Hammers joint-chairman David Sullivan, has been in the role for four years.
During that time Sullivan has helped the side grow after they successfully applied for a licence to play in the top tier of the restructured Women’s Super League in 2018.
In their first year competing in the WSL, the Hammers came seventh and reached the final of the Women’s FA Cup.
When Sullivan departs, general manager Aidan Boxall, who joined the club in April 2020, will take on greater responsibility in the day-to-day management of the women’s setup.
West Ham’s commercial director, Nathan Thompson, will oversee the continuation and growth of that area.
“This has been a very tough decision but, after much consideration, I believe it is the right time to move on,” said Sullivan.
“My time working with the women’s team has been a fantastic and hugely rewarding experience.
“When I look back on where we were four years ago, I am extremely proud of the team and the progress and improvements that we have all made since then.
“I feel we have put foundations in place that will give the women’s team a great chance of going on to bigger and better things in the future, and I want to thank every single one of the players, coaches, staff, fans and the partners who have been alongside me on this journey.
“Despite the fact that I am stepping down from the role, I will also continue to be the team’s biggest fan, supporting them in everything they do and helping in any way I can – this will include the playing budget being increased for next season.
“We’ve seen fantastic growth in the women’s game and I really do encourage even more people to get behind it, whether that be following your team on social media, watching your first game on TV or coming down to a game and supporting in person.
“That will be hugely important to ensure the women’s game continues to grow and flourish – something we all want.”