The NCP confirmed Bashir’s decision to quit the leadership of the party in a statement put out on Friday.
He was handing over the reins to his deputy, Ahmed Harun who takes charge as the interim chairman of the NCP until its general congress a date for which has not been scheduled.
Bashir’s resignation comes amidst unrelenting protests by Sudanese calling for him to step down as the country’s leader.
Human rights groups have accused the government of a brutal crackdown of the protesters.
At least 45 of them have been killed in almost three months of angry protests, while hundreds are still detained.
Bashir in power since leading a successful coup in 1989, has accused western capitals of formenting the unrest in his country.