Mr Doherty has represented West Tyrone as an abstentionist MP for the past 16 years.
The party has selected Barry McElduff, a member of the Northern Ireland Assembly, to stand in the 8 June poll.
Sinn Féin has four MPs but they do not take their seats in the House of Commons, in protest against British rule in Northern Ireland.
Sinn Féin's Pat Doherty has confirmed he will not be standing as a candidate in the upcoming general election.