He limped out of Saturday's Championship play-off final, sparking fears that he would play no part on Brazil this summer.
Kranjcar lasted just 33 minutes against Derby County at Wembley before being forced from the field.
A hamstring problem prevented him from completing that contest, and has now dashed his World Cup dreams.
A statement posted on the Croatian Football Association's official Twitter account read: "Croatian midfielder Niko Kranjcar will miss the World Cup due to hamstring injury."
National team doctor Boris Nemec told Jutarnji list: "Niko Kranjcar has ruptured his hamstring.
"The rupture is some inches wide and will need between four and six weeks to heal."
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