Boss Kenny Jackett admitted he is sorry to see Mikey Harris leave Pompey.
The Blues’ Academy coach is set to join Brighton & Hove Albion and will undertake a similar role at their Category 1 youth set-up.
The popular figure joined his hometown club in 2014, after previously being manager at Salisbury.
Harris has helped nurture the likes of Adam May, Ben Close and Brandon Haunstrup into the first team, after working with them in the academy.
Jackett saluted Harris’ hard work over the past three years and wished him good luck for the future.
The Pompey boss said: ‘Mikey has had a big input in the under-18s and the whole youth policy in the past few years.
‘We are sorry to lose him. We are a Category 3 academy and he goes on to a Category 1 at Brighton with their under-18s squad and we wish him all the best.
‘The club understand the reason behind him going and he is someone who has had a big influence in our youth policy.
‘We will be looking to continue his good work.
‘He’s had an input in the careers of Adam May, Ben Close and Brandon Haunstrup, who are now in the first team.
‘It’s very good for him getting to a Category 1 academy. They have fantastic facilities at Brighton.
‘They are in the Premier League and have started the season very well.
‘I think their aspirations will be to continue their progress – they’re not going to settle for where they currently are.
‘It looks a good club to go to. They’re a big club, and in terms of their own academy they will be hoping to produce their own players at the top level.
‘We’re disappointed Mikey will leave us.
‘He has done very well for Portsmouth in recent years and we wish him all the best.’
Harris was appointed manager at Salisbury when he was just 29 and became England’s youngest full-time manager at the time.
Jackett feels the fledgling coach has the attributes to be a Football League manager in the future.
He added: ‘People have their own aspirations and you can do very well staying as an academy coach.
‘Where or when you step out to first-team football very much depends on what he could want to do.
‘He’s been manager at Salisbury before and it depends on your own mentality as first-team football is a ruthless business.’