Austin Treacy, from Belfast, was given the accolade at the national Civil Service Awards.
Under Mr Treacy, the award organisers say levels of self harm at Hydebank were reduced while relationships between staff and those in their care were “transformed”.
“As governor, it is my privilege to lead a large, multi-disciplinary and talented team,” Mr Treacy said.
“Unlocking all their potential to achieve amazing results has been the highlight of my long career in the Northern Ireland Prison Service. Together, we implemented the first move from a young offenders’ institution to a college in the British Isles.
Linfield v Portadown Sunday clash: Breakers of the Sabbath will answer to God
NI Weather: 45 pictures of how we enjoyed wall-to-wall sunshine
Thousands expected to take part in 'Derry Day' this weekend
Esmond Birnie: The protocol is not as claimed boosting growth in Northern Ireland
Crawfordsburn Country Park: Five PSNI officers injured bringing crowd of 600 under control - two teens arrested - parents asked to know where their children are
“I know it is a cliché to say this was a team effort but that is the case. The positive changes would not have been achieved without the support of Prison Service senior managers and colleagues.
“This award also recognises the excellent work of the deputy governor Richard Taylor, and the entire team at Hydebank Wood. I also want to highlight the positive attitude of those in custody who have engaged with us to deliver the secure college.”
Justice Minister Claire Sugden gave her congratulations, saying: “Austin showed great commitment to transforming Hydebank Wood from a young offenders’ centre into the first secure college in the UK and this award is testament to his leadership.”
Sir Jeremy Heywood, Cabinet secretary and head of the Civil Service, said: “I always take great pride in the work of civil servants. Well done Austin.”