The world number four, who had pledged his allegiance to Ireland for the Games, has announced in a statement he will not be available.
McIlroy is one of a number of high-profile golfers to pull out with Adam Scott, Louis Oosthuizen, Charl Schwartzel, Marc Leishman and Vijay Singh having already said they will not travel to Brazil.
McIlroy said in a statement: “After much thought and deliberation, I have decided to withdraw my name from consideration for this summer’s Olympic Games in Rio de Janeiro.
“After speaking with those closest to me, I’ve come to realise that my health and my family’s health comes before anything else.
“Even though the risk of infection from the Zika virus is considered low, it is a risk nonetheless and a risk I am unwilling to take.
“I trust the Irish people will understand my decision. The unwavering support I receive every time I compete in a golf tournament at home or abroad means the world to me.
“I will continue to endeavour to make my fans and fans of golf proud with my play on the course and my actions off it.”