On repatriation to the Delhi Police in February 2002, Neeraj Kumar was posted as Joint Commissioner of Police / Special Cell, responsible for tackling terrorism. During this tenure, he conducted several counter terror operations, many of which led to the neutralization of notorious Pakistani terrorists. These included the encounters at Ansal Plaza, Tughlaqabad Fort, Deenpur Village in Najafgarh, Millennium Park and Lotus Temple. Thereafter he was posted as Inspector General of Police/Mizoram.

As the Director General of Police, Goa, he launched a sustained campaign against illegal immigrants, drug mafia and the Russian mafia indulging in land grabbing, human trafficking etc. He masterminded the arrest of Tariq Ahmed Batlo, a Pakistan trained Kashmiri terrorist, who was tasked with an assignment to cause Bali like bombings in Goa. Serious terror incidents were prevented in the holiday haven as a result of this arrest.

On his return to Delhi Police on transfer, as Special Commissioner of Police, he was responsible for the entire planning and execution of the police and security arrangements for the Commonwealth Games 2010, which have been widely appreciated.