Klopp oversaw the Reds' title success in 2019-20, ending a 30-year wait for a top-flight championship.
FIFA recognition for 2020 follows his win in the same award 12 months earlier after Liverpool won the Champions League.
'I'm really proud of the club' 🤗— Liverpool FC (@LFC) December 17, 2020
Shocked at the result, delighted for his staff and wishing the club’s current good moment to continue for as long as possible ✊
Enjoy Jürgen Klopp's interview moments after winning #TheBest FIFA Men’s Coach 2020 award 👇
The Liverpool manager pipped Hansi Flick, the Bayern Munich coach, and Leeds United's Marcelo Bielsa on this occasion.
Flick came up short despite guiding Bayern to the treble, with glory in the Bundesliga, DFB-Pokal and Champions League.
Remarkably, he was still assistant to Niko Kovac on July 20, 2019 when the period under consideration for the award began.
Klopp clearly anticipated a Flick win in the top coaching award as he responded to Thursday's announcement with surprise.
"I am [shocked]," he said. "I was just sitting here because last year I won it, so then I show everybody the respect when I'm nominated and show up wherever it is."
Told again at the end of his acceptance speech that he was The Best FIFA Men's Coach, Klopp replied: "I'm not but I won the award, so that's good enough."
Liverpool moved back top of the Premier League on Wednesday with a dramatic 2-1 home win over title rivals Tottenham.