They were wanted in separate cases, a top ATS official said.
Jitendra Singh Toni was wanted for supplying illegal arms to inmates who fled Nabha Jail in Patiala in November 2016, IG UP-ATS, Aseem Arun, said.
He was arrested from Mailani area in Lakhinmpur Kheri, he said.
Satnam Singh, on the other hand, was arrested by the joint team of the ATS, Punjab and local police from Sikanderpur area of the district.
Superintendent of Police, Kheri, S Channappa, told PTI that a Punjab court had issued warrants against them.
Pro-Khalistan terrorist outfits Babbar Khalsa International, International Sikh Youth Federation, Khalistan Commando Force and Khalistan Zindabad Force have been banned by the Union Home Ministry under the Unlawful Activities (Prevention) Amendment Act, 2004.