Ms Fong was previously the agency's chief legal adviser, and replaced Una Jagose, who is left the GCSB to become Solicitor-General.
Ms Jagose presided over the agency at a time of increased transparency and a push to improve public relations, after its activities came under intense scrutiny following a series of revelations and allegations.
A wide-ranging review of the SIS and GCSB, headed by former Deputy Prime Minister Sir Michael Cullen and lawyer Dame Patsy Reddy, was released this month.
The Prime Minister said Mr Hampton was a respected senior public servant, and his leadership and experience would help strengthen the GCSB.
"His broad experience will also help continue the process of more closely connecting and integrating the security and intelligence agencies with the wider public service."