Molango told the Congress, the highest trade union event in the UK, that greater player involvement in decision-making is key.
"Our members need to be central to this process – shaping the future of the game both for those who play now, and for those who will follow in their footsteps," Molango said in Liverpool.
"A seat at the table is no use when the decisions have already been made."
The PFA's plea comes after former player Karen Carney's UK government-commissioned review in July called for an overhaul of the women's game to increase professionalism, and amid the Lionesses' dispute over bonus structures and commercial payments offered to the World Cup squad.
"We want our legacy to be that we leave the women's game in a better place for those who follow us. That includes contracts, conditions and protections for players," Lucy Bronze, who helped England to a runners-up finish at the Women's World Cup, said in a statement.
"There is still a long way to go in the women's game, and now is the time for everyone to work together to make the experience of being a professional footballer as positive as it can be."
Molango urged fellow trade unions to support the implementation of recommendations from Carney's review, including the need to establish a Professional Football Negotiating and Consultative Committee (PFNCC) for the women's game.
The PFNCC, a committee of stakeholders including the players' union, already exists in the men's game. The government is expected to publish its response to the recommendations in the review later this year.
"There's so much changing in the women's game right now," said Lioness Katie Zelem, who is a member of the PFA's Players' Board. "Lots of it is really positive, but it's important that the players are part of that process and that we get to have our voices heard.
"We want to be partners in taking the game forward. There are structures in place in the men's game which mean players know they will be listened to. We need it to be the same for us."
England's female players do not have the same protections around contracts and conditions fought for and won by their male colleagues, and do not benefit from the same collective bargaining agreements that are in place in countries such as the United States and Australia.
The Lionesses' talks with the FA around bonuses - paused during the World Cup - are expected to resume later this month.
