Khawaja has been a vocal critic of a crackdown on 2011 protests that led to her opposition leader father Abdulhadi al-Khawaja being jailed for life.
She was arrested when she arrived at the airport on August 30 and charged with assaulting two policewomen.
She denies the charge, which carries a penalty of up to five years in prison, and counters that she was attacked by police.
The travel ban was imposed when she was granted bail on September 18.
The court accepted her lawyer's request that it be lifted taking into consideration her work commitments abroad, the judicial source said.
Khawaja heads the Beirut-based Gulf Centre for Human Rights and, like her father, has Danish citizenship. She has been a familiar figure in Washington, regularly meeting members of Congress and administration officials.
In 2011, she testified as a witness at a congressional hearing on Bahrain.
Her father was jailed following Shiite-led protests that year against the Gulf state's Sunni minority rulers.
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Meanwhile, police detained Rajab after questioning him over tweets considered insulting to a state institution, according to the interior ministry.
Rajab acknowledged that he was responsible for the remarks posted on his Twitter account, and "legal measures have been taken to refer him to the general prosecution," a ministry statement said.
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It said Rajab "insulted official bodies in his tweets".
In one tweet Sunday, Rajab charged that Bahrainis allegedly joining Islamist extremists in Syria were originally members of the Sunni-ruled kingdom's security forces.
"Many men who joined & came from security institutions and those institutions were the first ideological incubator," he wrote, referring to one acronym for the Islamic State jihadist group.
Rajab, who heads the Bahrain Centre for Human Rights, was released in May after serving two years in jail for participating in unauthorised protests.
He had led anti-government protests following a crackdown on Shiite-led demonstrations against the Al-Khalifa ruling family in March 2011.
US-based Human Rights First condemned Rajab's detention, urging the Gulf monarchy to stop "systematic harassment" of human rights activists.
"Reports that Maryam's travel ban is being lifted are good news, but we are alarmed that the Bahraini government continues to target prominent human rights defenders in an effort to impede their vital work," said the head of HRW's human rights defenders programme, Brian Dooley.
The watchdog said Rajab returned to Bahrain Tuesday after speaking at the United Nations in Geneva.
Tiny but strategic Bahrain, home to the US Navy's Fifth Fleet, remains deeply divided three years after the protests were crushed.
It continues to witness sporadic protests which often spiral into clashes with police.