"My biggest concern about the transfer was the shortfalls this may cause in our bilateral efforts to [combat] HIV/AIDS," Lugar said in a statement.
"The leaders I met with this week expressed their confidence that the money is a worthy investment, and given their strong leadership I have decided to lift my hold on the transfer funds."
Created in 2002, the Global Fund is the world's largest international financing project against AIDS, but has seen trouble because of the poor economy and corruption scandals.
Lugar led the Senate Foreign Relations Committee when the PEPFAR passed Congress in 2003. He currently serves as the panel's ranking Republican.
“HIV/AIDS relief, in the form of programs such as the President’s Emergency Plan for AIDS Relief, has a history of bipartisan support," he said.
"It is important for these programs to continue with support from both Republicans and Democrats."