Gomez, 25, revealed on social media this week that she had to undergo the operation after her kidneys were damaged by the autoimmune disease Lupus, which she has long battled.
Gaga, 31, sent her love and support to the star as she continued to recover after her best friend, actress Francis Raisa, 29, donated one of her organs, reports dailymail.co.uk.
Gaga tweeted: "Prayers and love to Selena Gomez. You are a warrior princess. What an inspiration."
She's not the only star to wish the "Fetish" singer.
"I think that she is a very strong woman. I'm very happy and proud of her," singer-actress Demi Lovato said.
Singer Nick Jonas wished her well too.