Badjie has been replaced by General Masanneh Kinteh, a former ambassador to Cuba and a special military adviser to Barrow since January.
As he took over from Badjie, Kinteh told reporters at defence headquarters in Banjul: "My immediate priority as chief of defence staff is to bring back the confidence in the troops to lift their morale."
He added that he wanted to boost civil-military relations, which have "eroded over the period as a result of the political impasse".
Barrow retook his oath of office on February 18, a month after he was sworn in across the border in neighbouring Senegal during a tense power struggle with his predecessor Yahya Jammeh.
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Jammeh had refused to step down following his defeat in December elections, but agreed to leave for exile on January 21 following negotiations with other west African leaders.
Barrow told the crowd at the swearing-in he would probe human rights abuses under Jammeh's iron-fisted rule spanning 22 years.
The United Nations and rights groups repeatedly condemned The Gambia's security services under Jammeh, blaming them for arbitrary detentions, extrajudicial killings and torture.
Last week Barrow removed the chief of the country's feared intelligence agency, Yankuba Badjie, and the head of the national prison system, David Colley.
Ousman Badjie, a Jammeh loyalist, had pledged allegiance to Barrow along with top defence, civil service and security chiefs on January 20, one day before the former president fled the country.
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