The president won a landslide victory in the election, grabbing almost 79 percent of the vote, Interior Minister Maria Fekter announced on television Sunday.
Controversial far-right candidate Barbara Rosenkranz came in second with 15 percent of the poll, with Rudolf Gehring of the small Christian Party scoring 5.4 percent for third place.
"I am extremely happy and thank the Austrian population for having so much confidence in me," Fischer said.
Rosenkranz had raised eyebrows by criticizing the country's anti-Nazi laws, saying they curtailed free speech.
The Austrian presidency is large representational post.