Černý was a member of the Czech under-17, under-18, under-19 and under-21 teams, being capped 23 times U17-U19 and 5 times U21 at national level.  During his international career, Černý played alongside the likes of Michal Kadlec and Tomáš Sivok.  Černý was part of the U-19 Czech Republic team that won Bronze at the European Championships in 2003. During this tournament, Černý kept a clean sheet against England in a 3:0 win.