His sole challenger Hama Amadou, imprisoned since November on shadowy baby trafficking charges, was flown to France days before the second round for medical treatment and the vote was marred by low turnout and an opposition boycott.
The electoral commission said Amadou got only seven percent of the ballots cast.
The election pitted 64-year-old Issoufou, a former mining engineer nicknamed "the Lion", against Amadou, 66, a former premier and parliament speaker known as "the Phoenix" for his ability to make political comebacks.
Amadou was forced to campaign from behind bars after being detained on November 14 on baby-trafficking charges he says were concocted to keep him out of the race.
Issoufou, who took office in 2011, campaigned on pledges to bring prosperity to the impoverished but uranium-rich country and vowed to prevent further attacks from jihadists in its vast remote north, and from Nigeria's Boko Haram Islamists to the south.
The West African state, where three-quarters of the population live on less than USD 2 a day, has only had a multi-party democracy since 1990.
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