This comes days after intelligence inputs had warned of a possible terror attack in the state by ISI-trained terrorists.
In a joint operation conducted by the UP Anti-Terrorism Squad (ATS), Military Intelligence and UP Intelligence, Aftab Ali was picked up from Faizabad, 120 km from here, this evening, IG ATS Aseem Arun said.
Aftab is believed to have received training from the ISI in Pakistan and was in constant touch with officials in the Pakistan High Commission, he said, adding that the ATS was in possession of strong evidence against him.
While Aftab was arrested, another suspect was taken into custody and was being questioned.
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In another statement late night, Arun said the UP ATS in a joint operation with its Maharashtra counterpart arrested Aftab's accomplice Altaf Qureishi from Mumbai.
Altaf was involved in Hawala transactions and had allegedly transferred money to the account of Aftab on the direction of ISI, the ATS said.
Rs 70 lakh cash has been recovered from Altaf, it said.
Aftab, son of Wajid Ali, is a resident of Khwaspura area of Faizabad, Arun said.
Aftab was also allegedly keeping a close vigil on the movement of troops in the area, especially between Faizabad and Lucknow, besides deployment of battalions, an ATS release said.
ADG (Law and Order) Aditya Misra said more information about the ISI network will be known through the mobile phone of the accused and more arrests are likely.
ATS sources said Aftab had gathered information on several army cantonment areas and defence establishments in the state.
Aftab is believed to have received training from the ISI in Pakistan and had contact with an official in the Pakistan High Commission and had also met him in New Delhi, Arun said, adding that the name of the official was being verified.
"He was in constant touch with Pakistan High Commission," the ATS statement said.
A government spokesman said tonight that the team led by ASP Rajesh Sahni will be awarded.
"The group, allegedly trained by Pakistan's ISI, has reportedly been asked to target Ayodhya (in Faizabad district), Varanasi, Vrindavan, and the Taj Mahal in Agra," UP police said.
Acting on intelligence inputs, security was upgraded at several religious places - including Ayodhya, Kashi and Mathura - and also at vital installations, including airports, bus and railway stations.
Taking cognisance of the intelligence warning that an ISI-trained group in the garb of Hindu seers might strike prominent religious sites in Uttar Pradesh, Chief Minister Yogi Adityanath had ordered construction of boundary walls around the holy spots.
The UP ATS has already alerted all district police chiefs and railway superintendents of police about the threat. "We are coordinating with other agencies to thwart such attempts," Arun said.
Central intelligence agencies have been sharing inputs with the UP Police since February about increased activity of terrorists in the state.
According to the latest alert, the ISI is planning to launch attacks in the northern state under the code name 'Operation Krishna India'.
"The agency (ISI) has reportedly trained the group for months to familiarise them with Hindu religious practices. Members of the module are planning to enter UP through the Nepal border in the guise of seers," the reports said.
Uttar Pradesh shares a 599.3-km open border with Nepal touching seven districts - Pilibhit, Lakhimpur Kheri, Bahraich, Sravasti, Balrampur, Sidhharthnagar and Maharajganj.
"As per the Intelligence inputs, the group has also been trained by Pakistan's ISI in Hindu religious practices, and might try to blend with the local populace before carrying out deadly strikes at prominent religious sites and other sensitive spots," police said.
The Intelligence agencies had picked up intercepts through electronic surveillance in which youths were heard discussing the deaths of banned Students Islamic Movement of India (SIMI) men in Telangana as well as IS suspect Saifullah in Lucknow.
In 2016, eight suspected members of SIMI had tried to evade the police by adorning saffron robes in Madhya Pradesh. The men were later killed in a police encounter.