The new agreement will cover the period up to and including the 2026 men's World Cup and the 2027 women's World Cup, it said in its statement.
FAW's announcement comes months after the United States women's national soccer team and their governing body US Soccer agreed to resolve a years-long dispute over equal pay in what players described as a landmark moment for the sport.
"We hope that this will allow future generations of boys and girls to see that there is equality across Welsh international football, which is important for society as a whole," the Wales men's and women's national teams said in a joint statement.
"With this agreement in place, we will now look ahead to the UEFA EURO 2024 and 2025 qualifying campaigns, as we aim to see further success across both our senior teams in the near future."
FAW said the announcement sends out the message to future players that anyone who represents Wales in the senior squads are "pulling on the same shirt and are representing the same team from an equal footing".
Wales' men's team were knocked out of the 2022 World Cup in Qatar in the group stage and are currently ranked 28th in the world. Their female counterparts failed to qualify for this year's World Cup and are ranked 32nd.
