In this paper, we develop a discrete-choice framework to quantify the economic benefits of Canada’s large-value payment system modernization (ie, the replacement of Canada’s large-value transfer system (LVTS) with Lynx, the new large-value payments system in Canada). We first estimate participants’ preferences for liquidity cost, payment safety and the network effect by exploiting intraday variations in the relative choice probabilities of the two substitutable subsystems (tranches 1 and 2) in the LVTS. Then, with the estimated model, we calculate the changes in participants’ welfare when the LVTS is replaced by Lynx. First, compared with the LVTS, Lynx has higher liquidity costs but is more secure. Second, when over 90% of current LVTS payments migrate to Lynx, there is an overall welfare gain. Third, accounting for equilibrium adjustment after the replacement of the LVTS with Lynx, about a 75% improvement in service quality level is needed to generate overall net economic benefits to participants. Among other things, adopting a liquidity-saving mechanism and reducing risks in the new large-value payments system could help achieve this improvement. Finally, the welfare changes are fairly heterogeneous across participants, especially between large and small participants.