Union Pacific Corp. plans to run its railroad with nearly 3,000 fewer workers this year as the company pushes ahead with a new operating plan that runs fewer, longer trains.

The Omaha, Neb.-based company said it plans to reduce its average number of workers by around 8% in 2020 after reducing its staffing by 11% in 2019. The railroad averaged around 37,500 workers during 2019 and nearly 42,000 during 2018.

Union...