Kerry will meet his counterparts from the Gulf Cooperation Council (GCC) as well as senior officials in the tiny but strategic island state situated between regional powerhouses Saudi Arabia and Iran.
He is the first US secretary of state to visit Bahrain, which is home to the US Fifth Fleet, since Hillary Clinton in 2010.
A State Department official said Kerry would discuss "ways that the Government of Bahrain can address some of the internal challenges and certainly to try to improve the overall political climate in Bahrain in terms of freedom of speech, freedom of religion".
Bahrain has been shaken by unrest since security forces crushed Shiite-led protests in 2011 demanding a constitutional monarchy and an elected prime minister.
Since then, dozens of people have been put on trial and handed lengthy jail terms in the Sunni-ruled kingdom over charges ranging from criticising authorities to planning or carrying out attacks.
The US official said that Kerry will meet Gulf ministers to discuss "some of the critical regional issues, primarily Yemen, Syria, the situation in Iraq, Lebanon, and elsewhere in the region."
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The GCC also includes the Sunni-dominated monarchies of Saudi Arabia, the United Arab Emirates, Qatar, Kuwait and Oman.
Saudi Arabia, Bahrain and the UAE have carried out air strikes against the Islamic State group in Syria as part of a United States-led coalition.
"We're satisfied, I think, with the overall level of support that we're getting from the Gulf states in the coalition," the US official said.
Several Gulf nations are also involved in a Saudi-led air and ground campaign in Yemen in support of exiled President Abedrabbo Mansour Hadi who has been ousted from the capital by Iran-backed rebels.
"We recognise that the focus on Yemen over these last months has detracted in some sense from the ability of the Gulf states to participate in the military components of the (anti-IS) coalition, although they are coming back and they are flying sorties again with us on that," the US official said.
Kerry will also ask Gulf nations to use their "influence on opposition groups" in Syria to maintain a fragile truce in force since February 27, according to another US official.
His visit aims to prepare for Obama's attendance of a GCC summit in Riyadh on April 21, where Washington's policies towards the Middle East are likely to come under the microscope.
Uneasy partners in the Gulf have been furious at Obama's engagement with their Shiite foe Iran and perceived retreat from the Middle East.