The country star, 58, sent a sweet note on Twitter to the pop star who also performed on Wednesday.
"@ladygaga You were fabulous today and everyday. A national treasure," Brooks wrote.
"Please tell Frederick and Miss Sarah thank you for me! They saved a cowboy today. Oh, and tell Miss Sarah to hug her momma for me! love, g," he added referring to Gaga's longtime makeup artist, Sarah Tanno, and hairstylist, Frederic Aspiras.
Brooks sang "Amazing Grace" after Gaga belted out the National Anthem.
For the ceremony, the Country Music Hall of Famer stuck to his Oklahoma roots and wore a black cowboy hat, black blazer, black shirt, dark denim jeans, and cowboy boots.
Brooks, a Republican, was personally invited to perform by first lady Dr. Jill Biden. On a zoom call with reporters earlier in the week, he made sure to note that his presence there was about bringing people together, not politics.
This wasn't the first time that Brooks performed at a presidential inauguration. He previously performed at Barack Obama’s 2008 swearing-in ceremony.
"I've played for every president there is, since Carter, with the exception of Reagan. This is an honor for me to get to serve... and it's one of the things that, if my family is around, no matter who the president-elect is, it's an honor to be asked," he told reporters, according to Entertainment Tonight.
Jennifer Lopez also performed at the ceremony with a rendition of "This Land Is Your Land." She also delivered the patriotic anthem "America the Beautiful."