[7] At the age of 15, he started playing for a local teagarden club (Binnaguri) in the Dooars area of West Bengal.

[7][8] Shaji Prabhakaran graduated from Lakshmibai National Institute of Physical Education (LNIPE), Gwalior in 1994.

[14] He started his career as a Senior Consultant at the Asian Football Confederation in 2017 following his long association with AIFF as Director of Vision & National Teams.

[16][17] In April, 2017 he got appointed as the President and then as Director of the Delhi-based professional I-League level club, Delhi United FC, which competes in the 2nd division.

[19][8] Prabhakaran has authored the book Back to the Roots: A Definitive Guide to Grassroots & Football Development.