Tanzania's National Electoral Commission on Friday declared Magufuli the winner of Wednesday's poll, after securing 84% of the vote against his rival Lissu of the Chadema party, with 13%.
In his bid for a second term, Magufuli has promised to boost the economy by completing infrastructure projects kick-started in his first term, such as a new hydropower dam, a railway line and new planes for the national carrier.
But the opposition and rights groups have complained that his administration has cracked down on critical voices, closing down media outlets and preventing opposition rallies.
The main challenger Lissu was shot 16 times in 2017 in what remains an unsolved case.
The government has denied stifling dissent.
The US has said it was concerned about “reports of systematic interference in the democratic process,” during the election.
The vote was marred by irregularities, including the use of force against unarmed civilians, pre-ticking of ballots, the detention of opposition officials and restrictions on political party agents accessing polling stations, the US Embassy said.