Issoufou beat Seyni Oumarou, a party ally of ex-president Mamadou Tandja who was ousted by soldiers last year for outstaying his term in office in the uranium-producing state.
“Overall preliminary results of the second round show as follows: Mahamadou Issoufou had 1,820,639 votes or 57.95 percent while Seyni Oumarou had 1.321248 42.05 percent of the vote ” Ghousmane Abdourahamane, chairman of the electoral commission told reporters.
Abdourahamane said about 3.3 million voters cast their ballots, representing a turnout of just 48 percent. Analysts said many Nigeriens have grown sceptical about politics after years of coups and corruption.
The military junta led by General Salou Djibo has won international praise for keeping its promise to organise credible elections to install a civilian president by April 6.
A desert nation whose uranium riches have drawn billions of dollars of investments, mainly from French nuclear giant Areva, Niger remains one of the world’s poorest countries.
It has suffered repeated coups since independence in 1960 and has recently faced attacks by local al Qaeda-linked militants.
West African regional body ECOWAS and African Union observers missions said on Sunday they were satisfied with the electoral process, adding that voting and vote counting had been carried out without any major incident.