He was also the coach for Negeri Sembilan FA gold cup team in 1992. He held the assistant coach position for the national Olympic team in 1997-1999 and 2002-2004.
In 2006, he was selected by Football Association of Malaysia to be the head coach for Malaysia under-23 side in the team preparation for the 2008 Olympic games qualifier. After winning the 2007 Merdeka Tournament, he was selected as the head coach for senior team by the FAM president Sultan Haji Ahmad Shah.
His first match as the head coach was the 2010 FIFA World Cup qualifier Asian zone against Bahrain. In the match, Malaysia lost 4-1 before draw 0-0 at Shah Alam. After ending the World Cup 2010 qualifying campaign, he then brought the under 23 side to the 2007 SEA Games in Thailand. The under-23 side also failed in the tournament after only managing 1 win, 1 draw and 1 defeat and for the first time since 1999 Malaysia failed to advance into the semifinal.
For 2008, Sathianathan bring the Malaysia best eleven to face Premier League giant Chelsea. Eventually the match was won by Chelsea by 2-0 and the squads did a good fight in the match as Chelsea head coach Luiz Felipe Scolari praise the Malaysia XI for giving a good fight against his team.
In 2008 Merdeka Tournament, Sathianathan again bring Malaysia into the final. Malaysia show impressive performance from the start of the tournament and did not conceded in all Merdeka Tournament match. However Sathianathan team lose 6-5 through a penalty shoot-out against Vietnam in the final.
In 2008 AFF Suzuki Cup, Sathia team start with convincing win over Laos. However in the last two matches, his team lost 2-3 to Vietnam and beaten by host Thailand 3-0. The lost against the Thai's saw Malaysia exit the competition for the first time since 1998. Rumors also spread that he will be replace by Indonesia former coach, Peter Withe because of his failure in 2008 AFF Suzuki Cup. However FAM decided to extend his contract for one more year with condition he must improve Malaysia FIFA ranking.
In February 2009, Sathia one year contract was terminated by FAM.