Fault rocks can function as barriers to subsurface fluid flow and affect the storage of CO2 in geological structures. Even though flow across faults often involves more than one fluid phase, it is typically modeled using only single-phase functions due to a lack of fault rock relative permeability data and complexities in incorporating two-phase flow properties into flow simulations. Here we present two-phase fluid flow data for cataclastic fault rocks in porous sandstone from the 90-Fathom fault (northeast England). The study area represents a field analogue for North Sea saline aquifers of Permian–Triassic age that are currently being considered for CO2 storage. We use the experimental data to populate a synthetic model of a faulted saline aquifer to assess the impact of these fault rocks on CO2 injection. We show that even fault rocks with low clay contents and very limited quartz cementation can act as major baffles to the flow of a non-wetting phase if realistic two-phase properties are taken into account. Consequently, pressure may increase far more rapidly in the storage compartment during CO2 injection than anticipated based on models that only incorporate absolute fault rock permeabilities. To avoid high pressures, which may lead to hydrofracturing and CO2 leakage, either more complex injection strategies need to be adopted or seismic data acquired to ensure the absence of faults in aquifers selected for CO2 storage.