Thomas Jones Synod College is located in Jowai, the District Headquarter of the West Jaintia Hills District, Meghalaya. The College was established with a vision of providing college education to young men and woman who wish to have their education under Christian auspices by the erstwhile Khasi Jaintia Presbyterian Synod vide its Resolution No. 34 (E) CED of the Synod meeting held during 13th - 17th of March, 1996 at the Balang Mawten, Rangthong Presbytery.

This College was particularly named after Rev. Thomas Jones, also known as the father of the Khasi Alphabet, who was the first missionary from the Presbyterian Church of Wales to set foot in the Khasi Hills at Sohra on the 22nd of June 1841. Naming the college after him is a humble token of commemoration for his significant and monumental contribution to the Khasi community, especially as the pioneer in the field of education.

As per the provision provided by the Indian Constitution, Thomas Jones Synod College was established by the Khasi Jaintia Presbyterian Synod, Mihngi in the year 5th August, 1997 as a Religious Minority Institution. The same has been confirmed as per Government No. EDN,811/86- “The Governor of Meghalaya is pleased to make the following rules governing the maintenance grant to Aided Colleges of Meghalaya”.

Reference 2(g) “Minority College” means a college established and administered by a religious or linguistic Minority having the right to do so under Clause (1) of Article 30 of the Constitution of India.

The Mission of this College is to provide its student with education of a high standard of scholarship and learning and to inspire and prepare them for selfless and dedicated service in any part of India as responsible citizens of the country. The motto of the college shall be "Tip Briew, Tip Blei" which literally means "Know Man and Know God". This motto calls upon one and all to be conscientious, humane, socially committed and spiritually inspired persons. It is expected that this motto shall be a guiding principle to all student who graduate from this institution.