Born in Hyderabad, Prabhu first came into prominence when he represented Mumbai, Thane and the Maharashtra State Team (Santosh Trophy). He went on to feature for Mumbai FC, PIFA and Kenkre FC in the MDFA Elite Division and other local tournaments following which he joined the youth academy at FC Pune City in 2018. Nikhil was retained by newly-minted Hyderabad FC when the FC Pune City franchise switched over to Hyderabad.
The now 21-year-old defender represented the club in the 2nd Division League in the 2019-20 season. The following season he didn’t feature in the ISL for HFC and was loaned out in January 2022 to Odisha FC. He ended up making three appearances for the Juggernauts in the recently concluded 2021-22 ISL.
Odisha FC liked what they saw of the defender and have made the signing permanent.