The 29-year-old suffered the injury during QPR's victory over Derby County in the Championship play-final on Saturday, and was substituted after 33 minutes at Wembley.
Kranjcar has been an integral part of his national team in recent years and was preparing for his second World Cup appearance.
However, the Croatian Football Association announced on Monday that the former Tottenham man, who has 81 international caps, will not travel to Brazil following an MRI scan in Zagreb.
"Croatian midfielder Niko Kranjcar will miss the World Cup due to hamstring injury," the body posted on their official Twitter account.
Kranjcar made his debut for the national team in August 2004.
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