Egypt returned a $500 million deposit to Qatar at the start of November after Qatar refused to renew it upon its maturity, a central bank official told Reuters on Monday.
The central bank expects to return a further $500 million in early December, the official, who declined to be named, added.
Qatar had deposited the funds with the central bank in late 2012.
Relations between the two countries deteriorated after the army ousted Islamist President Mohamed Mursi in July. Qatar had been a firm backer of Mursi's Muslim Brotherhood and lent or gave Egypt $7.5 billion during the year he was in power.
In September, Egypt returned $2 billion that Qatar had deposited with its central bank, after talks to convert the funds into three-year bonds broke down.
Saudi Arabia, Kuwait and the United Arab Emirates promised Egypt a combined $12 billion in aid in July.