We adopt a boundary integral method to study the dynamics of a translating droplet confined in a Hele-Shaw cell in the Stokes regime. The droplet is driven by the motion of the ambient fluid with the same viscosity. We characterize the three-dimensional (3D) nature of the droplet interface and of the flow field. The interface develops an arc-shaped ridge near the rear-half rim with a protrusion in the rear and a laterally symmetric pair of higher peaks; this pair of protrusions has been identified by recent experiments (Huerre et al., Phys. Rev. Lett., vol. 115 (6), 2015, 064501) and predicted asymptotically (Burgess and Foster, Phys. Fluids A, vol. 2 (7), 1990, pp. 1105-1117). The mean film thickness is well predicted by the extended Bretherton model (Klaseboer et al., Phys. Fluids, vol. 26 (3), 2014, 032107) with fitting parameters. The flow in the streamwise wall-normal middle plane is featured with recirculating zones, which are partitioned by stagnation points closely resembling those of a two-dimensional droplet in a channel. Recirculation is absent in the wall-parallel, unconfined planes, in sharp contrast to the interior flow inside a moving droplet in free space. The preferred orientation of the recirculation results from the anisotropic confinement of the Hele-Shaw cell. On these planes, we identify a dipolar disturbance flow field induced by the travelling droplet and its $1/r^2$ spatial decay is confirmed numerically. We pinpoint counter-rotating streamwise vortex structures near the lateral interface of the droplet, further highlighting the complex 3D flow pattern.