Mullen met Bahrain’s King Hamad al-Khalifa and Crown Prince Salman, whom the United States has praised for taking "positive steps" to placate protesters.
"Obviously Bahrain has been important to us for decades," he said.
The United States bases its Fifth Fleet in Bahrain.
A visiting US politician said the US Fifth Fleet should remain in Bahrain despite the unrest.
"I have faith in the people of Bahrain and I have faith in our military. This is crucial to world commerce and international security," Republican Representative Joe Wilson told French press agency AFP.
Security forces were not in evidence Manama’s Pearl Square on Friday, while protesters continued to camp there.
"We will not accept any dialogue with he who kills us in cold blood," said one banner.
Leading Shia-Muslim clerics have called on the demonstrations to mourn the victims killed by security forces, urging protesters to march en masse to Pearl Square.