The Agape Church first began as a cell group gathering in an English speaking International Church. The International Church was part of the Uniting Church of Australia, located in Sydney CBD. The cell group gathering grew in numbers and in 1990 it was named as the 'Indonesian Fellowship' under the leadership of Mr. Stephen Tanuwijaya. 

The Indonesian Fellowship held regular Sunday services. Due to its rapid growth it was suggested that the Indonesian Fellowship become an Indonesian Church affiliated with the International Church, and that a pastor who has been trained and ordained, should be appointed. 

Discussions with the senior pastor of the International Church continued for around 3 years. However despite initial expectations, a satisfactory resolution could not be reached. After much prayer and fasting, as well as seeking signs from God, on 30 December 1997 God answered through various signs. Discussions were resumed with the local senior pastor and subsequently, Mr. Stephen Tanuwijaya surrendered himself in faith to become a Minister and servant of the Lord, to lead the Indonesian Church separately from the International Church. 

By the grace of our Lord Jesus Christ, with prayer and fasting, and after receiving encouragement from various fellow ministers, a new church called Agape Indonesian Christian Fellowship (Jemaat Kristen Indonesia) was formed on 19 March 1998 and registered with the Department of Fair Trading. The first service was held on 29 March 1998 at the Central Trinity Lutheran Church building, 17 Valentine Street, Haymarket with an initial congregation of no more than 50 people. 

On 22 May 1998, Mr. Stephen Tanuwijaya was ordained by Rev. Virgo Handojo of the Indonesian Christian Church International (JKI!), and endorsed by The Pacific Southwest Mennonite Conference, California USA. In 1999 the Agape Church became affiliated with Churches of Christ, in New South Wales Australia and the Synod of the Indonesian Christian Fellowship (JKI).