As electrification works progressed northwards along the line, direct services from Tel Aviv were made possible without the need for a transfer at Ben-Gurion Airport and as a result the station's ridership rankings rose further – making it the fifth-busiest railway station in the country and the busiest outside of Tel Aviv (immediately above the previous holder of this title, Haifa Hof HaCarmel) with 1,651,659 passengers boarding or disembarking in 2020.

In 2021, 3,598,443 passengers embarked and disembarked, not only surpassing the (2019) pre-COVID traffic numbers, but also making Navon station the fourth-busiest in the network, above Tel Aviv University.

Due to the constraints of building the Tel Aviv–Jerusalem railway in a grade suitable for carrying passengers, the station platforms had to be built 80 metres (260 ft) below street level, at the end of a tunnel leading to the railroad bridge over Emeq HaArazim.

The station can double as a shelter in case of a conventional, biological or chemical attack, being able to provide refuge for 5,000 people.

As of 2022, additional surface entrances from the east and south are being added as part of a major urban re-development plan being carried out in the vicinity of the station.