The 19-year-old has been rewarded for his consistent performances in both Premier League 2 and the Leasing.com Trophy with fresh terms, and finalised the deal before linking up with the Czech Republic Under-21 squad.
He saved a late penalty to earn three points against Fulham's Under-23s last month and produced a Man-of-the-Match performance in the Leasing.Com Trophy win at Lincoln City.
Kovar joined the club during the winter transfer window in 2018 from FC Slovacko.
He will look to maintain his development in Neil Wood's side and continue to hone his talents behind the scenes.