"The head of one man has been blown off," Bashir Ahmed, deputy police superintendent told Reuters news agency.
Another of the dead men had his legs blown off, while the third had his stomach ripped open and died later in hospital, he added.
At least two of the dead men were students at a nearby madrassa, suspected of having links to Sipah-e-Sahaba Pakistan, a banned Sunni Muslim group, the deputy superintendent said.
Police and security agencies have been on maximum alert since an attack outside a five star hotel in Islamabad on January 26 that killed a guard.
There have been a series of suicide bomb attacks in Pakistan in recent weeks, and police have also arrested several suspected would-be suicide bombers.
More than 40 people have been killed in suicide attacks since mid-January.