Airports Company South Africa has lifted the suspension of SA Express, with flights resuming on Friday afternoon.
The airline was grounded earlier this week amid mounting financial and operational woes.
According to ACSA, SA Express was grounded because of outstanding debt, but it said that the airline made a partial payment towards settling its debt.
However, ACSA declined to disclose how much it was owed by SA Express.
Airline spokesperson Mpho Majatladi said operations resumed from around midday on Friday, adding that their staff will continue to offer assistance to passengers.
"Customers can also contact our customer care department for assistance. SA Express apologises and regrets the inconvenience that this has caused to all its passengers," she said.