João Pavão Martins graduated in Mechanical Engineering at the Instituto Superior Técnico in 1976. While still a student, he began teaching at IST in 1974. With a Fulbright scholarship he studied at the State University of New York at Buffalo, where he received his PhD in Artificial Intelligence in 1983. He obtained the Aggregate Professor title from Instituto Superior Técnico in 1991 and has been a full professor at IST since 1993.

In 1984 he created a student group at IST that dealt with the teaching and research in Artificial Intelligence. Many of the members of this group are currently professors at the Departments of Computer Science and Engineering and Electrical and Computer Engineering.

He was one of the proponents for the creation of the Degree in Computer Science and Engineering (LEIC) at IST, of which he was the coordinator between 1997 and 2002. In LEIC he was responsible for the scientific area of Artificial Intelligence from its creation until his retirement in 2022.

He was one of the proponents of the creation of the Computer Science and Engineering Department of IST, of which he was President between 2003 and 2004 and between 2009 and 2010 and Vice-President between 1998 and 2002.

In 1986 he was one of the founders of SISCOG, the first Portuguese company dedicated to the development of Artificial Intelligence applications, the dean company of the IST Spin-off community, of which he has been a Director since its foundation.

He is considered the "father" of Artificial Intelligence at Instituto Superior Técnico. In 1997, 2003 and 2012 he received the Innovative Application Award given by the Association for the Advancements of Artificial Intelligence (AAAI), of which he is a senior member. He is the author of one book published by Wadsworth Publishing Co. (USA), one book published by McGraw-Hill de Portugal, one book published by College Publications (UK) and four books published by IST Press, two co-authored, as well as co-editor of several international conference proceedings.

He was awarded the Medalha de Mérito Científico in 2023, an initiative of the Ministério da Ciência, Tecnologia e Ensino Superior. The medal was presented during the Encontro Ciência 2023.

On October 29, 2024, he was honoured with the title of Emeritus Professor of Universidade de Lisboa.