Indian Institute of Management Kozhikode was instituted in 1996 by the Government of India as the fifth Indian Institute of Management in collaboration with the Government of the state of Kerala. In 1997, the first batch of 42 students in the Post Graduate Program (PGP), equivalent to MBA, commenced at the temporary campus at the National Institute of Technology Calicut. In 2000, the site of the present campus at Kunnamangalam was identified. The following year, Joseph Stein (also the architect of the India Habitat Centre in Delhi) and Stein Mani Chowla Architects began the design and construction of the institute. In 2003, IIM Kozhikode moved into its hill-top campus. The then President of India, APJ Abdul Kalam and the then Chief Minister of Kerala, Mr. A.K. Antony, inaugurated the campus.
Interactive Distance Learning, an online management education programme for working executives, was introduced in 2001-02. IIM Kozhikode was the first institute in Asia to offer a distance learning programme in management for working executives. Management Development Programme was also introduced the same year. The institute increased the number of students in PGP to 180 in 2005.In the batch of 2013 the intake is going to be around 400 for PGP. IIMK started its doctoral programme, Fellow Program in Management(FPM) in 2007. The intake of women in the PGP course was pro-actively increased to 30% from batch of 2010-12 to improve the number of women in management roles in India. In 2010, IIMK signed a memorandum of understanding with Yale University to establish a Center of Excellence for Academic Leadership as part of Singh-Obama Knowledge Initiative.