England were pushed into an early change after injury ended Eric Dier’s time on the field and was replaced by Ross Barkley on 17 minutes.
Despite the injury setback, the Three Lions raced ahead after Raheem Sterling tapped home Jadon Sancho’s square delivery on 25 minutes.
Following a dry passage of play, England’s advantage increased after Harry Kane powered home from the penalty spot following a foul on Sterling in time added on.
The Czechs shuffled their wits with a substitution right from the restart as Burnley's Matej Vydra came on for Jakub Jankto.
England appeared jaded in the earlier phases of the second half, as Czech closed in on a comeback with David Pavelka’s close-range shot on 53 minutes.
Any hopes of a comeback were dashed on 62 minutes, as a cool and composed finish by Sterling gave the hosts a three-goal cushion.
Sterling completed his hat-trick six minutes later after his curler from outside the box wrong-footed Jiri Pavlenka.
The 2018 World Cup semi-finalists added a fifth after Tomas Kalas turned home Callum Hudson-Odoi’s initial effort on 84 minutes as the encounter ended 5-0.