The effects of long duration ground motions on the seismic performance of a newly constructed two-storey balloon-type cross-laminated timber (CLT) building located in Vancouver, Canada, was studied. A three-dimensional numerical model of the building was developed in OpenSees. The connection and shear wall models were validated with test data. Twenty-four pairs of long and short duration records with approximately the same amplitude, frequency content, and rate of energy build-up were used for nonlinear dynamic analyses. Fragility curves were developed based on the results of incremental dynamic analysis to assess the building’s collapse capacity. At design intensity level, ground motion duration was shown not to be a critical factor as the difference in inter-storey drift ratio between the two sets of records was negligible. However, due to the larger number of inelastic cycles, the long duration motions increased the median probability of collapse by 9% when compared with the short duration motions. Further research is required to evaluate the duration effects on taller and platform-type CLT buildings.