Droplet migration in a Hele–Shaw cell is a fundamental multiphase flow problem which is crucial for many microfluidics applications. We focus on the regime at low capillary number and three-dimensional direct numerical simulations are performed to investigate the problem. In order to reduce the computational cost, an adaptive mesh is employed and high mesh resolution is only used near the interface. Paramet-ric studies are performed on the droplet horizontal radius and the capillary number. For droplets with an horizontal radius larger than half the channel height the droplet overfills the channel and exhibits a pancake shape. A lubrication film is formed between the droplet and the wall and particular attention is paid to the effect of the lubrication film on the droplet velocity. The computed velocity of the pancake droplet is shown to be lower than the average inflow velocity, which is in agreement with experimental measurements. The numerical results show that both the strong shear induced by the lubrication film and the three-dimensional flow structure contribute to the low mobility of the droplet. In this low-migration-velocity scenario the interfacial flow in the droplet reference frame moves toward the rear on the top and reverses direction moving to the front from the two side edges. The velocity of the pancake droplet and the thickness of the lubrication film are observed to decrease with capillary number. The droplet velocity and its dependence on capillary number cannot be captured by the classic Hele–Shaw equations, since the depth-averaged approximation neglects the effect of the lubrication film.