The two men were killed in separate incidents within a span of a few hours on October 22.
The three accused, Rashid, Golu and Rashid alias Waseem, were arrested from Sambhal, Uttar Pradesh, in the last couple of days, the police said.
On October 22, a man named Wazid was shot dead in Zaffrabad and he died on the spot. On the same day, a man named Arif Hussain was also shot dead in Bhajanpura.
Following the two killings, teams of northeast district, Special Cell and Crime Branch were working on leads to arrest the accused.
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Nupur Prasad, Deputy Commissioner of Police (Shahdara), said they were conducting raids in Sambhal when it was learnt that the suspects involved in northeast Delhi's killings were also hiding there. A raid was conducted and they were nabbed.
During interrogation, they revealed that they have been involved in multiple crimes such as robbery, armed robbery, murder, snatching in Delhi, UP and Tamil Nadu, the DCP said.
It is suspected that the October killings were the result of personal enmity.