To further ease up traffic in the expressway, the NLEX adopted an "open" and "closed" systems designed to significantly increase the hourly throughput of the tollway, particularly in high-traffic environments.

The open system runs from Balintawak to Bocaue, where traffic concentration is heaviest. A fixed rate of P42 is charged in the open system, regardless of where the motorist exits at any point between the Balintawak and Bocaue toll plazas. This one-stop-only form of toll collection substantially reduces the time spent for toll booth stops and greatly eases traffic flow in the concerned urban areas especially during peak hours.

The closed system, on the other hand, runs through the remaining 70-kilometer section of the expressway, from north of Marilao to Sta Ines, Pampanga, where there is lower traffic count. Here, the motorists pay the additional toll fee of P2.49 per kilometer upon exiting the NLEX.