Cardiff head coach Matt Sherratt has been appointed to lead the team in the final three matches of the 2025 Six Nations.
"The WRU and Warren have agreed that making this change now is in the best interests of the Wales squad as it continues to compete in the 2025 Six Nations tournament," WRU chief executive Abi Tierney said in a statement.
"We are grateful to Warren for all he has done for the game in Wales. He remains our longest-serving and most decorated head coach in terms of the silverware he has won."
Gatland was reappointed for his second stint in charge of Wales in December 2022 after winning three Six Nations Grand Slams and reaching two Rugby World Cup semi-finals during his first spell.
"I would like to thank the WRU board for the faith shown in me after a tough campaign throughout 2024 and for affording me the time and resources to try to turn things around for this 2025 tournament," said the New Zealander.
"We have worked hard, we have a talented young squad that is developing and have been desperate to turn potential into results but now is the right time for a change."