Issoufou will bid for a second term on March 20 on a promise to clamp down on Islamist militants in what is one of the poorest countries in the world.
His opponent is a former prime minister who came second to Issoufou's 48.4 percent with 17.8 percent. Amadou has been in prison since November on charges relating to baby-trafficking. He says he is innocent and a victim of political repression.
Critics say Amadou's imprisonment is part of a crackdown by the government over the election season. The government says it respects the law and such criticisms are politically motivated.
Following the results, Issoufou congratulated the people of Niger for the peaceful election. "I also salute my adversaries in the first round and congratulate them for the quality of the debate," he told journalists.
A coalition of four parties agreed before the election to back the candidate that came second in a bid to defeat Issoufou.
Those parties gained a cumulative vote of about 38 percent, though it was unclear which side had an advantage ahead of the second round or how Amadou would campaign from prison. Turnout was nearly 67 percent, the National Electoral Commission said.
Niger is under threat from Nigeria-based Islamist militant group Boko Haram, which has staged a series of cross-border attacks in the southeastern Diffa region, forcing the government to impose a state of emergency there.