The pop star wrote alongside the picture: "I'm thinking of you today during this tragedy."
She later re-tweeted a message from one of her followers saying that one of her fans had died in the blaze.
The message read: "A Little Monster died in a tragedy here in Brazil! His name is Luiz Felipe! Mother Monster Pray for him! @ladygaga #PrayForSantaMaria +181."
Lady Gaga tweeted in response: "My heart is with you Brazil,
"Sending my prayers to the families and friends who lost loved one in the fire in Brazil. Im thinking of you today during this tragedy."
The scale of the tragedy has shocked Brazilians.
The country has declared three days of national mourning for the people killed in the fire, which tore through the Kiss nightclub in the southern city of Santa Maria.
Many of the victims were reportedly students from the city's federal university.
The first funerals were due to be held on Monday morning.