"We were doing the first part of the prayers when we heard the blast," said Kamal Jaafar Hassan, a worshipper."
The blast has occurred as the Saudi lead a coalition of Arab states in an air campaign against Shia rebels in crisis hit neighbouring Yemen.
Shia Muslim minority in Saudi Arabia mainly reside in eastern province and there have been sporadic protests by Shia there for greater rights. This would be the first such attack on a Shia mosque there.
Saudi Arabia has also been threatened by Islamic State (ISIS), which is being targeted by an international coalition including the Sunni kingdom.
No one has claimed responsibility for the attack.