Hoodbhoy widely writes about the role and modernisation of Pakistan military, particularly the defence budget spending by the Pakistan government on the military. In an interview on secularism, he mentioned that obsession with scientific-religious apophenia may have caused lack of scientific advancement among Muslims in recent years. In 2003 he was one the signers of the Humanist Manifesto. Hoodbhoy criticized the partition of India, calling it an "unspeakable tragedy" that "separated people who at one time could live together in peace".