Christ Church in Alexandria, Virginia will take down a memorial marking the pew where Washington sat with his family, saying it is not acceptable to all worshipers.
"The plaques in our sanctuary make some in our presence feel unsafe or unwelcome," leaders said, a reference to the fact that Washington was a slaveholder.
"Some visitors and guests who worship with us choose not to return because they receive an unintended message from the prominent presence of the plaques."
"Many in our congregation feel a strong need for the church to stand clearly on the side of 'all are welcome- no exceptions,'" they concluded.
A memorial to Confederate Gen. Robert E. Lee will also come down.
The decision comes in the wake of renewed controversy over whether statues honoring Civil War figures should be no longer honored. The debate broke out again over the summer after a white nationalist rally in Charlottesville, Virginia killed one and injured others.
President Trump expressed concern that the censoring of Confederate generals would lead to dishonoring Thomas Jefferson and George Washington as well.