Opposition activists say security officers beat him on the back, head and neck at a rally on Friday.
Bahrain's interior ministry denies the attack but the US is calling on it to fully investigate the allegations.
The US Fifth Fleet is stationed in Bahrain and the two countries have close ties.
The interior ministry has said police found Mr Rajab on the ground and took him to hospital.
It has released a video of the events, showing what it says was an unauthorised demonstration in the capital, Manama.
The US State Department said the facts of the case were in dispute, but that in general it was very concerned "about frequent reports of excessive force by the police".
It is unusual for Washington to publicly chastise Bahrain, despite considerable international criticism of the harsh crackdown against anti-government protesters over recent months, says the BBC's Rajesh Mirchandani in Washington DC.
Even though the US wants to support democracy movements in the Middle East, Sunni-led Bahrain is a key ally against Iran's Shia influence, our correspondent adds.
Shia anger
Bahrain's King Hamad recently agreed to implement reforms after an independent commission found detainees were abused and even tortured to death.
Bahrain's Shia Muslim majority has been campaigning for greater rights in the kingdom since last February.
Confrontations between security forces and demonstrators occur almost daily.
Last spring, more than 40 people died in a heavy-handed government crackdown against protesters in the Gulf kingdom. An independent commission later concluded that "excessive force" had been used.
The violence has fuelled anger in Shia areas against the Sunni ruling family and political elite.
