The drop-off zone will be extended and a new anti-clockwise traffic system will clearly separate the area from the rest of the car park.
Network Rail hopes that this will to help ease congestion at busy times.
Safety will also be enhanced as a new walking route with marked pedestrian crossings will be installed.
There will also be a new zebra crossing at the entrance to the car park with speed bumps on the approach.
The car park will need to be closed overnight from 11.30pm until 5.30am between Monday January 31 and Friday February 18 while this work takes place.
The drop-off point will remain in use throughout to minimise the impact on passengers.
Leeds Station Manager for Network Rail, Nick Cooper, said: “We’re making important changes to improve safety for both drivers and pedestrians using our short-stay car park.
These improvements will help traffic flow better and make it easier for our passengers to catch a train or leave the station, especially during busy times.
“I’m sorry to anyone who is inconvenienced by the overnight closures and encourage passengers to speak to a member of the station team if they need any help.”
Further work to improve the short-stay car park at Leeds station will follow later in 2022.