The effect of wakes on a separated boundary layer over a flat plate is investigated by direct numerical simulation. The flow separates due to a strong adverse pressure gradient induced by suction along the upper simulation boundary. The forcing Strouhal number St = fL(x)/U-ref of the wakes ranges from 0 to 2.9. Each forcing pulse generates three roll-up vortices, which originate near the separation point and convect with approximately half the local free-stream velocity. The separation and reattachment points vary with the forcing frequency, the size of the separated region is shortened significantly for high forcing frequencies, but no other significant variations of the mean boundary layer properties are observed unless the separation bubble is allowed to fully reform. The separation lengths of the periodic cases can be estimated from a single recovery experiment in which the forcing is suddenly removed.