As railway markets are increasingly deregulated, coordinating and prioritising between capacity requests becomes more complex and more important. This paper describes the advantages and challenges of different allocation methods in vertically separated open-access railway markets, with several railway operators and heterogeneous traffic, and where a public infrastructure manager must resolve operators’ conflicting path requests. Three broad groups of allocation methods are described: administrative methods, allocation by social cost-benefit analysis and willingness-to-pay based allocation. We describe pros and cons of these allocation principles for three different market segments: commercial traffic with long planning horizons, (subsidized) traffic controlled by public transport agencies, and traffic with short planning horizons. We then outline an allocation process that meets the requirements of a deregulated market better than conventional methods. It is a mixed method, which uses an auction-like mechanism to allocate pre-defined paths to commercial operators on specified, capacity-constrained lines. The net social benefits of capacity reserved for traffic controlled by public transport agencies is assessed through social cost-benefit analysis of timetables. The benefits decrease when timetables are adjusted to make room for additional commercial train paths; the size of this loss determines the reservation price of the auction-like mechanism. Dynamic pricing is used for short-term allocation on congested line segments.