Cost-benefit analysis (CBA) for cycling infrastructure investments are less sophistically developed compared to the ones for private cars and public transport, and one of main reasons is the lack of “well-developed” transport models for cycling. In this study, a dedicated transport model for cycling is used to appraise cycling infrastructure investments in Stockholm, Sweden. The model captures the impact of a change in cycling infrastructure on cycling route choice, mode choice, destination choice and trip generation and calculates cycling flow on link level. the generalised cost measure defined in the route choice model captures the impact of cycling infrastructure. Results suggest that although cycling flow on the links with investment may increase substantially, only a small share comes from modal shift and thus the external effects such as reducing car congestion and emissions are marginal. For all three scenarios investigated, over 97% of the benefits measured in the unit of generalised cost belong to the existing cyclists. The route choice model does not minimize travel time but generalised cost which also measures health, safety benefits and other possible benefits that may be considered by the cyclists when they choose to cycle. In fact, travel time saving benefits of the investments evaluated in this paper are all negative. The existing effect evaluation models therefore need to be adjusted to be more consistent with the transport model.