In July 2003, with the help and support of CYANT, two fleets left Darwin; the first group of 24 yachts went to Kupang and a second group of 23 yachts left for Bali one week later with the intention that they would link up in Bali for a combined party/presentation. This did not eventuate as the yachts that went to Kupang found that the marine beauty of the Eastern Part of Indonesia had a lot to offer and they went cruising! In some ways this could be consdiered the start of what is now called Sail Indonesia.

In February 2005, the Indonesian sailing foundation Yayasan Cinta Bahari Indonesia (YCBI) announced that a second stopover after Alor had been arranged at Riung on the island of Flores featuring a festival and cultural displays.  Rally entry papers were sent out during the last week in March and soon sixty yachts had entered.  Within 4 weeks of entries being open 70 yachts had registered and the event was closed to further entries.

In an attempt make this rally a truly international event in 2005, an inaugural follow-on rally was arranged following the route up the west coast of Malaysia leaving Singapore with the Malaysian island of Langkawi as its destination.  This event had the full support of the Malaysian Government’s Tourism Department.   The rally was a success and was repeated again in 2006 and 2007.
In 2006 the Sail Indonesia event attracted 96 yachts; in 2007, 110 yachts participated.