The accused fell sick and fainted near Barabanki border and was rushed to district hospital where doctors declared him dead this evening, he said.
He was also an accused in 2007 Gorakhpur blasts.
Meanwhile, UP chief minister Akhilesh Yadav ordered a probe into the death, an official spokesman said in Lucknow.
The inquiry would be conducted by a committee of a secretary (home) and an ADG or DIG level officer.
On April 26, the Uttar Pradesh government had filed a plea to withdraw cases against Khalid Mujahid and another accused Tariq Qasmi in 2007 serial blasts in Lucknow, Faizabad and Gorakhpur.
However, on May 10, a special court in Barabanki rejected the UP government's plea. They were arrested on December 20, 2007 with arms and explosives.
The UP government had requested the court that it wanted to withdraw the case in "public interest and for the sake of communal harmony," but did not defined both the words.