He graduated from Fairview High School in 1988,[1] subsequently receiving a BM from the Berklee College of Music in 1992[2] and an MM in jazz composition from Chicago's DePaul University in 1998.

The two would continue to collaborate often, releasing the albums Black Water, Mother Tongue and Codebook with Mahanthappa's quartet, and Raw Materials as a duo.

He would later travel to India on a grant to work with Gopalnath; the two played together in concert between 2005 and 2008 and collaborated on the album Kinsmen (2008), which fuses Western and Indian approaches to improvisation.

[1] Mahanthappa further claims The Brecker Brothers, The Yellowjackets, David Sanborn, Grover Washington, Jr., and Miles Davis' electric bands as influences in creating Samdhi.

He leads or co-leads the Rudresh Mahanthappa Quartet (with Vijay Iyer or Craig Taborn on piano, François Moutin on bass, and Dan Weiss on drums), Raw Materials (with Vijay Iyer), Indo-Pak Coalition (with Rez Abbasi on sitar-guitar and Dan Weiss on tabla), MSG (with Ronan Guilfoyle on bass and Chander Sardjoe on drums), Dakshina Ensemble septet, and various groups playing under the label Dual Identity.