The boats will depart from District 1 and take five to six hours to reach Con Dao, an archipelago comprising 16 pristine islands around 230 kilometers away.
The fare will be around 900,000 ($39.42).
The city Department of Transport said the high-speed boats would help meet the growing travel demand.
Currently travel between Saigon and Con Dao Island is only possible by air. Only two airlines, Bamboo and Vasco, operate flights on the route and round-trip fares range around $155-170.
Waterway transport companies Greenlines DP and Phu Quoc Express JSC have applied to operate the service.
Con Dao is famous for its beautiful beaches and a wartime prison.