Danny Cowley has agreed a long-term deal to remain as Portsmouth's head coach despite missing out on the League One play-offs on the final day of the season.
Cowley, who took up the reins in March with Pompey sitting in 10th place in the division, has accepted chairman Michael Eisner's offer of an extended stay at Fratton Park, as has his younger brother and assistant Nicky.
In a statement on the club's official website, the pair said: "It has been one of the greatest privileges of our lives to be associated with this club.
"In the short time that we have been here, we have seen the love and passion that the people of Portsmouth have for this football club. With the support of Michael and the board of directors, we will create a team that you can be proud of.
"For this club, today is about new beginnings.
"While we will always take learnings from the past, we are absolutely determined to live in the moment and enjoy the challenges that this journey will bring."
Eisner, who drafted in the Cowley brothers after Kenny Jackett's near four-year reign drew to a close after the Papa John's Trophy final defeat by Salford, said: "We are thrilled to continue with the Cowley brothers leading our team on the pitch.
"Their dedication and hard work, plus their exciting style of play, makes them a perfect match for Portsmouth and our fans."
Portsmouth went into Sunday's last game of the campaign sitting in the final play-off place, but a 1-0 home defeat by Accrington, coupled with Oxford's 4-0 demolition of Burton saw Karl Robinson's men snatch sixth place and Pompey slip to eighth after Charlton's victory over champions Hull.
The Cowleys have previously worked together at Concord Rangers, Braintree, Lincoln and Huddersfield.