Metalworkers union Numsa has served Comair with a 48-hour strike notice.
The union says the dispute relates to wage disparities at the airline that were raised last year.
Numsa says it cannot allow a situation where the principle of equal pay for work of equal value is blatantly violated in the workplace.
Spokesperson Phakamile Hlubi-Majola says the strike on Thursday will affect Comair flights.
“We’ve had several meetings with the employer this year, where we’ve made proposals around this issue. Unfortunately, the management of Comair rejected our proposal. They’ve proposed that high earners be denied wage increases, until the salaries of other workers catch up.”