It said the king issued a decree granting the activist "a special pardon for health reasons", but without elaborating.
In May, an appeals court upheld a six-month prison sentence for Rajab, a member of Bahrain's Shiite majority arrested in April, for insulting public institutions on Twitter.
Rajab, 51, was sentenced in January over comments he posted about the interior and defence ministries in the Sunni-ruled monarchy.
In one of the messages deemed offensive, Rajab charged that many Bahrainis fighting with jihadists in Syria were former Bahraini security forces personnel who had developed Sunni extremist views while in service.
The activist, who has led anti-government marches and heads the Bahrain Centre for Human Rights, had previously served two years in jail for taking part in unauthorised protests and was freed in May 2014.
Bahrain, home to the US Navy's Fifth Fleet, has been rocked by unrest since security forces crushed Shiite-led protests in 2011 demanding a constitutional monarchy and an elected prime minister.
Washington has called for Rajab's release, while international rights groups have condemned the trials against opponents of the Sunni regime.
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