President Pranab Mukherjee rejected a mercy petition from Mohammad Afzal Guru and he was hanged at 8 a.m. (0230 GMT) in Tihar jail in the capital, New Delhi, officials said.
India blamed the 2001 attack on the parliament of India.
"This is only about the law taking its course," Home Secretary R.K. Singh told reporters after the execution.
Barricades were erected and hundreds of police and paramilitary forces were deployed in major towns of Indian occupied Kashmir.
Five militants stormed the heavily guarded parliament complex in New Delhi on Dec. 13, 2001, armed with grenades, guns and explosives, but security forces killed them before they could enter the main chamber.
Ten other people, most of them security officers, were killed.
Guru, an Indian national, was convicted for helping organise arms for the attackers and a place for them to stay.