Hunt replaces David Rutherford, who announced he would not be seeking reappointment in May this year.
As well as Hunt's appointment, Little has announced the appointment of Dr Saunoamaali'i Karanina Sumeo as Equal Employment Opportunities Commissioner.
She has extensive experience in the public sector, working as principal policy advisor at Oranga Tamariki and before that, held positions at Ministry of Social Development, the Ministry of Pacific Island Affairs and the Tertiary Education Commission
She takes over from former National MP Jackie Blue.
"Each commissioner brings a wealth of experience in improving human rights both nationally and abroad," Little said.
"Their experience, leadership and fresh perspective stood out amongst some distinguished applicants, and are deemed to be the best candidates to take the commission forward."
He said he looked forward to working with both the commissioners to tackle some of the most pressing issues facing New Zealanders.
The final vacant commissioner position will be filled in the coming weeks, Little said.
The process and panels used to appoint commissioners is independent and complies with the Paris Principles.
The leaders of all political parties represented in Parliament were consulted.