Jacob Ramsey’s goal was the difference between the two sides as England began their journey on the front foot.
Hosted in Georgia and Romania from 21 June to 8 July, England are one of 16 teams fighting for the European Championship title.
But it was Czech Republic who almost took the lead, denied only by Trafford who pushed away Vasil Kusej’s left-footed shot.
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But despite a first half of end-to-end football, neither team could find the back of the net.
However, it took England less than a minute of the second period to break the deadlock.
Anthony Gordon’s pass to Ramsey allowed him to slot the ball past Vitezslav Jaros in the 46th minute.
Czech Republic almost replied immediately.
Seconds after the restart, Trafford made a crucial save to deny the opposition an equaliser.
England thought they had doubled their lead part way through the second half through a Gordon goal, but the referee pulled back play for a foul by Morgan Gibbs-White.
England’s defensive line, led by captain Harwood-Bellis, continued to be tested but could not be broken down by a lively Czech Republic attack.
Emile Smith-Rowe sealed victory four minutes into added time to make it 2-0.
Fellow City players Tommy Doyle and Cole Palmer were unused substitutes.
