[12] A year later, he relocated to the Almaden center in Silicon Valley to become the senior manager of the computer science principles and methodologies department of IBM Research until 2000.

[14][12] His research group focused on algorithms, complexity theory, cryptography, text mining, and other fields.

[15] After working 14 years at IBM, he became senior vice president and chief technology officer at enterprise search vendor Verity in 2004.

's chief strategy officer by CEO Carol Bartz, who replaced the co-founder Jerry Yang in 2009 and was fired in 2011 as the company declined.

[citation needed] In 2000, he was named a fellow of the IEEE;[24] received the Best Paper Award at the ACM Symposium on Principles of Database Systems;[25] and received the Best Paper Award at the Ninth International World Wide Web Conference (WWW9).

[28] In 2008, Prabhakar was made a member of the National Academy of Engineering,[29] and in 2009, he was awarded a Laurea honoris causa from the University of Bologna.

In 2017, Prabhakar and co-authors received the Seoul test of time award for their 2000 paper "Graph Structure in the Web" at the WWW conference.