Mr Said Abdullahi Deni was declared the winner in the third round of voting in the region's parliament after beating 20 other candidates.
Mr Deni garnered 35 votes closely followed by former intelligence chief Mr Asad Osman Abdullahi, who got 31 votes.
The former Planning Minister who unsuccessfully contested the Somali presidency in 2017 takes over from the Gaas administration which was rocked by allegations of graft, nepotism and insecurity.
Somalia's five regions - Puntland, Galmudug, Hirshabelle, South West State, and Jubaland - have been holding presidential elections progressively from November to end of 2019.
The South West State went to the polls in November and Hirshabelle is next after Puntland.
Despite becoming semi-autonomous in 1998, Puntland, an oil rich state, is yet to achieve universal suffrage.
The region is also often entangled in territorial disputes with the self-declared republic of Somaliland.
Mr Deni will lead the region until 2023.