Dr Kuti, who was accompanied by his wife, running mate Ibrahim Abdi and hundreds of his supporters at the county tallying centre during final announcement of the results.
They immediately went into celebrations, bringing the town to a standstill for hours as they rejoiced after their victory.
In his acceptance speech, the governor-elect pledged to fulfil his campaign pledges and to boost cohesion between locals in the cosmopolitan region.
“My administration will work closely with security forces to ensure that there is peace to pave way for development,” he added.
Dr Kuti has previously worked in the government as Minister for Youth Affairs in 2005 and also as Minister for Livestock from 2008-2013.
He said he will work with all elected leaders in shaping the county’s destiny for the next five years.
He further pledged to involve all communities in decision-making.