Jim Crawford's side produced some decent patches of play but were ultimately undone by sloppy defending in the first half in particular.
The Czechs opened the scoring in the 17th minute when Christian Frydek burst through from midfield and fired in a thumping strike from just outside the box.
Ireland were unlucky not to level within two minutes when St Patrick's Athletic winger Josh Hogan cut in from the left and fired goalwards. His strike was tipped over by keeper Petr Mikulec.
The Irish did level in the 22nd minute when a deep Thomas Byrne corner was nodded down by Aaron O'Driscoll and Bohemians defender Warren O'Hora spun cleverly to finish to the bottom corner.
Unfortunately the Irish defence was caught napping as the Czechs regained the lead within 60 seconds. A break down the left ended with Frydek firing past Mark Travers when the ball was cut back to him in the penalty area.
Czech captain Antonin Rusek made it 3-1 in the 38th minute when he headed to the net from a well hit corner but it was an avoidable goal which frustrated Irish coach Jim Crawford.
Anthony Scully was unlucky not to pull one back two minutes into the second half when he linked well with Kian Flanagan before producing an excellent strike that thumped off the Czech crossbar.
Five minutes later Shamrock Rovers striker Dean Dillon had a header saved from a cross by the impressive Flanagan. Despite a strong second half display the Irish could not breach the Czech defence again and now turn their attention to tomorrow morning's meeting with Russia. The Russians beat Turkey 5-0 in the other game in Group A.
"Overall the performance had a lot of positives but unfortunately we conceded some sloppy goals and that's an area we will be aiming to improve upon as the tournament progresses," said Irish Head Coach Jim Crawford.
"Some of our attacking play was pleasing and, for many of the players, they are still getting to know what this level is all about so this experience will be invaluable.
"The Under 19 coach Tom Mohan was in attendance today and the players know that they are playing to make an impression upon him for next season. Performances in games such as this can only help their cause."
Republic of Ireland: Travers; McKenna (A Byrne 41), O'Hora, O'Driscoll (McSweeney 67), O'Sullivan (Mollett 41); Keaney, Nicell, Flanagan, Keena (N Byrne 41); T Byrne (Dillon 41), Hogan (Scully 41).
RESULTS & FIXTURES
Monday, April 24: Czech Republic 3-1 Republic of Ireland, Modranka
Tuesday, April 25: Republic of Ireland v Russia, Dunajska Luzna (KO 10:00)
Thursday, April 27: Republic of Ireland v Turkey, Dunajska Luzna (KO 10:00)
Friday, April 28: Classification match, TBC