"Birthday greetings to @HillaryClinton. May Almighty bless her with a long life and good health," he tweeted.
Clinton turned 67 today.
Modi had met Hillary along with her husband, former US President Bill Clinton, on September 29 during his visit to Washington.
The Clinton couple had a 45-minute meeting with Modi, who was accompanied by External Affairs Minister Sushma Swaraj.
Hillary was Secretary of State in the previous Barack Obama administration.