The arrest came in the midst of Pakistan Interior Minister Rehman Malik's ongoing visit to India.
The suspect, Rajendra Chaudhary alias Samandar Das, allegedly planted bombs in two coaches of the Samjhauta Express along with Kamal Chauhan, who is already under arrest.
Police have secured a transit remand for Mr Das and will produce him today at the Panchkula courts near Chandigarh, where the Samjhauta Express case is being heard.
On February 18, 2007, two blasts had ripped through coaches of the Samjhauta Express near Panipat, when the train was heading from Delhi to Lahore.
The blast is alleged to have been carried out by right-wing extremists. The National Investigation Agency, which probes terrorism cases, has chargesheeted six people, including Swami Aseemanand and Sadhvi Pragya Thakur.