Mr Boutcher, who had been serving as interim chief constable, has more than 35 years' experience as a police officer.
He previously served as the former chief constable of Bedfordshire Police and led the Operation Kenova investigation. The Northern Ireland Policing Board confirmed the appointment on Tuesday.
Speaking about the appointment, Board chairwoman Deirdre Toner said: "I am pleased to confirm that Jon Boutcher QPM is the successful candidate from this appointment competition. Jon takes on the leadership role for one of the most important public sector services in Northern Ireland.
"He is clearly committed to the challenges ahead, to tackling crime and criminality and to providing a policing service that is community based and focused on delivery to the public.
"There are also significant pieces of work to be progressed to manage and mitigate the serious financial pressures currently facing policing, and deal with confidence and other issues arising from recent events."