Starting from next year, 50% of the system's energy will be provided by wind farms, rising to 70% in 2016 and 95% in 2017, according to the deal agreed with Vivens, the rail operators' energy procurement joint venture.
By 2018, all of the 1.4TWh of energy used to power the country's trains will be sourced from wind projects that are completed this year or later rather than just purchased on the energy market.
"The underlying aim is to avoid procuring energy from the limited existing number of sustainable energy projects in the Netherlands as this would ramp up market prices... and at the same time [we aim] to boost the process of generating green power," the company said.
Eneco estimates that the rail network's energy use equates to the power from around 500MW of wind projects.
Some of the energy will come from Eneco-owned projects, while the rest will be supplied to the company under long-term power purchase agreements.
At least 50% of the energy must be sourced from within the Netherlands, while the remainder can be procured from new projects outside the country.
A spokesperson for the company said that it is considering sourcing power from offshore projects that are due to go online. Eneco's own 129MW Luchterduinen offshore project is due to come online in 2015, but the company was unable to confirm that energy from this project would go towards powering the rail network.