After his retirement from playing, Fandi worked as a coach. He started as the assistant to Singapore's national coach, Vincent Subramaniam, for the 1999 SEA Games, where Singapore finished fourth. In 2000, Fandi became coach of SAFFC and guided them to the S.League title, and he won the S.League Coach of the Year Award. Under Fandi, SAFFC ended the 2001 season without winning a trophy and were 2002 S.League champions by a 20-point margin. Fandi then simultaneously served as assistant national coach, helping Singapore win the Tiger Cup in 2005, and coach of the Young Lions, which rose from the bottom of the S.League in 2003 to two third-place finishes in 2004 and 2006.