The Connecticut Department of Transportation (CTDOT) owns the tracks and stations within Connecticut, and finances and performs capital improvements. MTA owns the tracks and stations and handles capital improvements within New York State.

The ownership of the tracks used by Metro-North Railroad is a split between state and private entities. In New York, the majority of the tracks (including the Hudson and Harlem Lines) are owned by the Metropolitan Transportation Authority (MTA), which acquired them from the defunct Penn Central railroad. However, in Connecticut, the ownership is different: the Connecticut Department of Transportation (CTDOT) owns the New Haven Line's main track from the New York state border to New Haven, as well as its branch lines. A significant exception exists on the New Haven Line between New Rochelle and the Connecticut border, where the tracks are owned and maintained by Amtrak as part of the Northeast Corridor. This complex patchwork of ownership means that while Metro-North operates the trains, they must often coordinate maintenance and scheduling with both state governments and federal rail authorities to ensure the safety of the millions of commuters who traverse these rails daily between the suburbs and Grand Central Terminal.