The deregulation of railway markets has brought new challenges to the capacity allocation process. In this context, we present a new hybrid methodology for allocating railway capacity to commercial train operators. Commercial freight or passenger train operators compete with each other as well as with subsidised local commuter trains. In the method presented in this article, minimal track access charges are computed using a social cost-benefit analysis of alternative commuter train timetables. These minimal charges are used as a starting or reservation price in an auction-based method for capacity allocation between the commercial operators. The aim of this study is to assess the use of such a welfare-based track access charging system in a real case scenario. On a congested line in the region of Stockholm, we evaluate the welfare-based access charges of commercial operators. We show that the new methodology can be used to allocate capacity between subsidized and commercial train operators. Moreover, we provide an estimate of the marginal minimal access charge per train path that the commercial operators request.