Following their domestic success, Hradec played in the 1960–61 European Cup and was eliminated by FC Barcelona in the quarterfinals, Barcelona eventually becoming runners-up. In 1995 Hradec won the Czech Cup and subsequently played in the Cup Winners' Cup, where it was eliminated in the round of 16 by FC Dynamo Moscow. In the 2002/03 season they were relegated to the Second Division. They returned to the top flight in 2009/10 only to be relegated once more in 2012/13; however they would place second in the 2. Liga signifying a return to the top division for the 2014/15 season.
Hradec played in the newly formed Czech First League from its inception in 1993 until being relegated at the end of the 1999–2000 season. Their best league finish in this time was 8th place, which they achieved in the 1998–99 season. The 1990s also saw the club triumph in the Czech Cup, winning the competition in 1995. This achievement saw the club qualify for the UEFA Cup Winners' Cup, where they were eliminated in the round of 16 by FC Dynamo Moscow.
The club returned to the top flight in 2001 after winning the Czech 2. Liga at the first attempt, securing promotion with four games to spare. After just two seasons though, the club again finished in the relegation places and were relegated back to the second tier. This time it was seven seasons before the club would achieve promotion, winning the 2009–10 Czech 2. Liga to secure their status in the top flight once more. Hradec equalled their best Czech First League finishing position of 8th in the 2010–11 season.