Pramod Singh Kushwaha, DCP, Special Cell Delhi Police addressed the press meet as informing.
Arrested Khan was present at Batla House, along with four others, on Sept 19, 2008 in Delhi's Jamia Nagar.
The 32-year-old's arrest by Delhi Police's Special Cell comes three weeks after the elite anti-terror force apprehended another suspected IM operative Abdul Subhan Qureshi (46), a software engineer-turned-bomb-maker, from east Delhi after a brief gunbattle.
Sources said Khan, after the shootout, spent several days travelling in trains and buses across Delhi and Uttar Pradesh and eventually managed to reach Nepal. His arrest dents the plan of reviving network of Indian Mujahideen. "After living in Nepal for a few years, both left for Saudi Arabia", the police officer said. A native of Uttar Pradesh's Azamgarh, Khan carried a bounty of Rs 15 lakh on his head.
Later, he came in touch with a Nepali resident Nizam and with his help crossed the Indo-Nepal border from Bihar into the Himalayan country, he said.
Kushwah said, "After fleeing from the Batla House encounter, he called his wife in Azamgarh and said, "Chota locha hua hai". Encounter specialist Inspector Mohan Chand Sharma lost his life during the operation.
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While Delhi Police had announced a reward of Rs 5 lakh for information about Khan, the National Investigating Agency (NIA) had announced a reward of Rs 10 lakh.
Some of Khan's accomplices had links with the Islamic State - the radical Islamist group, the police said. Qureshi was arrested last month by Delhi Police.
Police said Khan managed to procure local identity cards and stayed in Nepal till 2014.
He returned to Nepal from Saudi Arabia in March 2017 and would occasionally travel to India.
"For a cover, he worked as a labourer and also met with many sympathizers there", Mr Kushwah said.