BCM was established as the Bible Institute of Malaya in 1960 to train national workers for the gospel. The first class of seven students graduated in 1962 - four men and three women. From the beginning, the emphasis of the college has been on a holistic training program for the full-time ministry of the gospel. A three-year Bible college diploma was offered.

At first the programs were offered in English. Students wishing to study in Chinese would go to Ecclessia Bible Institute in Hong Kong. Between 1968 and 1972, several students were able to do their studies in Chinese under the direction of Rev David and Alice Nyien. However, a full fledged Chinese department was formed only in 1980.

In 1982, the name was changed to the Bible College of Malaysia with the introduction of the Bachelor of Theology program. A Certificate of Biblical Studies for lay leaders was started in 1986.

BCM was accredited by the Asia Theological Association (ATA) in 1989. In 1990 BCM became the first chartered member of the Asia Pacific Theological Association (APTA). BCM was accredited by APTA between 1994-1999. BCM is also a founding member of the Malaysian Association of Theological Schools.

BCM is also a member school of Asia Graduate School of Theology (Malaysia/Singapore/Thailand) [AGST-MST], a consortium of theological colleges and seminaries offering quality post-graduate programs to prepare scholars and leaders to equip the church in Asia.

In 2003, the Bahasa Malaysia department was formed. The College has started two graduate study programs, the Master of Ministry in 2004 and the Master of Divinity in 2008.

In addition, BCM partners with several institutions to provide specialized training:

• Global Training Ministries founded by Kevin and Glenys Hovey, offering World Harvest Institute, a 6-week missionary training program;
• Seminari Theoloji Malaysia and Malaysian CARE, offering the Certificate in Social Ministry
• Christian Heritage College and Malaysian CARE, offering the Diploma in Counseling Studies

To help train leaders for the local churches, BCM also has several extension centers throughout Malaysia offering courses in all three languages.