Palace spokesman Ari Dwipayana said here the president and his entourage left the country at 07.00 local time on Tuesday from Balis international airport of Ngurah Rai, using the presidential plane.
It is the first state visit by an Indonesian president to the countrys former province.
In Dili the president will meet with his Timor Leste counterpart President Taur Matan Ruak and Prime Minister Maria De Araujo.
The main agenda in the talks between Jokwoi and Timor Leste leaders are cooperation in trade, investment , energy development , infrastructure development and settlement of border issue.
The Timor Leste government would award President Jokowi the highest service medal of Grande Colar de Ordem de Timor Leste .
The two governments would sign five memorandums of understanding on cooperation in youth and sports, search and rescue, energy , petroleum and mineral resources.
Before returning to Indonesia, the president and group would visit the Metinaro and Seroja military cemeteries.
The president and group are expected to arrive in Jakarta at 20.00 local time on the same day.
Including in the pressidential entourage are Coordinating Minister for Economy Darmin Nasution, Foreign Minister Retno Marsudi, Marine and Fisheries Minister Susi Pudjiastuti, Youth and Sportsd Minister Imam Nahrawi, and Cabinet Secretary Pramono Anung.