PSS Sleman needed 24 years before they could play in the top division of Indonesian football. In 2000, PSS Sleman finally fulfilled its dream to join the Indonesian elite teams in Divisi Utama (it was the top division before the restructure of the Indonesian Super League). During 2000-2006, PSS Sleman managed to secure their existence in the top division. Fourth position in 2003 and 2004 season and semifinalists of Indonesian Cup 2005 were the best achievements they gained during that period. In 2006, the biggest earthquake in modern era strucked Special Region of Yogyakarta. More than 5000 people died and thousands people lost their house and properties. For this condition, PSS Sleman and two other teams from Special Region of Yogyakarta (PSIM Yogyakarta and Persiba Bantul) agreed to withdraw from the national competition. For this force major condition, PSSI (Football Association of Indonesia) decided to give dispensation for those three teams. PSSI nullified the relegation and those three teams finished 2006 season in last place.
The year of 2007 became one of the milestones of PSS Sleman history. In that year, PSS Sleman started to use their new stadium, Maguwoharjo Stadium as their home base. This stadium was built as the response of Sleman government to support PSS Sleman as the representative of their city in national league. As an addition, in 2002 till 2003, PSS Sleman rented Mandala Krida Stadium as their home base in Yogyakarta. They left Tridadi Stadium in Sleman for the more representative and bigger in capacity stadium.
After two years rented Mandala Krida Stadium, Sleman government then took the decision to build their own stadium as new asset and investment in Maguwoharjo. Though in 2007 it had not finished yet, PSS Sleman started to use Maguwoharjo Stadium as their new home base. PSS Sleman played their first match in Maguwoharjo Stadium in 2007 season versus Pelita Jaya. PSS won 2-1 with goals from Ferry Setiawan and Slamet Nurcahyo. Unfortunately, PSS Sleman failed to follow up on this good result. In the end of the season 2007 which initiated the professionalisation of the Indonesian Super League, PSS Sleman failed to secure access to Liga Super Indonesia (LSI) as the top division. In 2008-2012, PSS Sleman played in Divisi Utama (DU). In that period, PSS Sleman failed to gain promotion. Last season (2011-2012), PSS Sleman finished in 7th position in the table.