Kottayam has long been at the forefront of literacy and education. In the 17th century, a Dutch school was started at Kottayam, which was short-lived. The first English school in Kerala, and the first college in India, was established in 1817 by the Church Missionary Society of England as CMS College. Kottayam became India's first town with 100% literacy in 1989. 

The Government Medical College, Kottayam, is one of the most prominent medical colleges in Kerala. Mahatma Gandhi University, Kerala, is based out of Kottayam. Kottayam boasts several other colleges and universities.

There are 14 engineering colleges. Government Engineering College, Rajiv Gandhi Institute of Technology, Kottayam is located in Pampady, 14 km east of Kottayam. Indian institute of information technology, Kottayam is an institute of national importance is also located around 30 km (19 mi) from Kottayam, near to Pala town.