The team originated from two clubs, the 1966-67 European Cup semi-finalist Dukla Prague, which tradition it carries, and FC Příbram, merged in 1996. Příbram had previously spent two seasons in the second division, having been promoted from the third-tier Bohemian Football League at the end of the 1993–94 season. Dukla Prague, on the other hand, had spent the previous two seasons in the Bohemian Football League after being relegated from the inaugural season of the Czech First League in 1993–94.
The club competed in the 1996–97 Czech 2. Liga, playing home matches at Stadion Juliska in Prague. The club won the league that season and won promotion to the Czech First League. In 1997 the club moved to Příbram, playing its matches at Na Litavce stadium. The club played in the top division, changing its name to FK Marila Příbram in 2000. The club spent ten consecutive seasons in the top flight until being relegated in the 2006–07 season. The club played in the 2007–08 Czech 2. Liga, reaching third place at the time of the mid-season break under manager František Barát. At the end of the season, the club celebrated promotion back to the Czech First League after just one season away. The club changed its name to 1.FK Příbram in 2008. Příbram played in European competition in the 2000 UEFA Intertoto Cup, reaching the third round of the tournament. After finishing fourth in the 2000–01 Czech First League, Příbram again played in Europe, overcoming French side Sedan in the 2001–02 UEFA Cup before losing to Greek side PAOK in the second round of the competition.