Manchester City pipped Liverpool to the Premier League title on Sunday, coming from behind to beat Aston Villa 3-2 at the Etihad Stadium to finish one point ahead of the Reds.
Liverpool finished on 92 points, going unbeaten at home all season.
Despite missing out on the title, the German tactician has been voted as the best in England and takes home the award for a second time; his first coming in the 2019/2020 season when he led Liverpool to the title.
Klopp also guided Liverpool to triumphs in the FA Cup and Carabao, and can add the UEFA Champions League to his list of laurels with victory over Real Madrid in the Champions League final on Saturday.
Also in the running the award were Crystal Palace boss Patrick Vieira, Newcastle United's Eddie Howe and Brentford gaffer Thomas Frank.
Klopp also took home the Sir Alex Ferguson trophy for the League Managers' Association(LMA) manager of the year, which is voted for by the managers across the four English divisions.
Reflecting on the climax to the Premier League season while accepting his award, Klopp said: "It is a great honour and it was an insane season. The last matchday when only two games were meaningless and, in the rest, we all played for absolutely everything.
"It was a bit nervy, it wasn't the best outcome for us, but we are already over it. And when you win a prize like this you are either a genius, or you have the best coaching staff in the world - I am here with four of my coaching staff, and they know how much I appreciate them."
The Liverpool manager added on the LMA prize: "This being voted for by my colleagues is obviously most important prize you can get.
"I don't believe in individual prizes in football generally, it is a team sport and I would be nothing without these boys there. It is all about what we can do together and what we did together."
