The expressway employs a combination of open road, closed road, and barrier toll systems.
Northbound toll collection is done upon entry at Sucat Exit, Bicutan Exit, and toll plazas such as Alabang Toll Plaza in Muntinlupa for light vehicles and Runway Toll Plaza in Taguig (near the Nichols Toll Plaza of South Luzon Expressway) for heavy vehicles, where vehicles from South Luzon Expressway (SLEx) are paid a toll based on their entry point there and exits on Skyway have no toll collection at all.
Southbound toll collection is done at the toll barriers upon exit; for those exiting to SLEx or Muntinlupa–Cavite Expressway (MCX), the toll collection is done on its exits instead.
No tickets are issued on entry points on Skyway.

Skyway employs the RFID-based Autosweep electronic toll collection (ETC) system used on the expressways under San Miguel Tollways.
Previously, the transponder-based E-Pass is used.
ETC collection lanes are usually on the leftmost lane of a toll plaza, but may occur on mixed lanes, where cash payments can be done alongside ETC.

As of August 2020, the toll rates (both cash and ETC) are as follows:
The expressway employs a combination of open road, closed road, and barrier toll systems. Northbound toll collection is done upon entry at Sucat Exit, Bicutan Exit, and toll plazas such as Alabang Toll Plaza in Muntinlupa for light vehicles and Runway Toll Plaza in Taguig (near the Nichols Toll Plaza of South Luzon Expressway) for heavy vehicles, where vehicles from South Luzon Expressway (SLEx) are paid a toll based on their entry point there and exits on Skyway have no toll collection at all. Southbound toll collection is done at the toll barriers upon exit; for those exiting to SLEx or Muntinlupa–Cavite Expressway (MCX), the toll collection is done on its exits instead. No tickets are issued on entry points on Skyway.
Skyway employs the RFID-based Autosweep electronic toll collection (ETC) system used on the expressways under San Miguel Tollways. Previously, the transponder-based E-Pass is used. ETC collection lanes are usually on the leftmost lane of a toll plaza, but may occur on mixed lanes, where cash payments can be done alongside ETC.
As of August 2020, the toll rates (both cash and ETC) are as follows:
Skyway (Metro Manila)