Leila Fourie replaces acting chief executive Andy White and will take on the new role on 12 September.
Ms Fourie makes the move from the Johannesburg Stock Exchange where she served on the board as executive director.
Her 20-year career – which included stints in Accenture and Standard Bank – has given her experience in consulting, investment banking, retail banking and capital markets positions in South Africa.
APCA chair Rob Craig praised Ms Fourie for her “strong track record of driving change and guiding industry initiatives”.
“The payments system is evolving rapidly and Leila is well-placed to lead [the] industry through this time of change,” Mr Craig said.
Meanwhile, Ms Fourie said she is looking forward to her new role.
“I am thrilled to be joining APCA at this exciting time in Australian payments and I look forward to engaging the market and making a contribution to the future payments ecosystem.”