We model the three-dimensional (3-D) crustal deformation in a deep pull-apart basin as a result of relative plate motion along a transform system and compare the results to the tectonics of the Dead Sea Basin. The brittle upper crust is modeled by a boundary element technique as an elastic block, broken by two en echelon semi-infinite vertical faults. The deformation is caused by a horizontal displacement that is imposed everywhere at the bottom of the block except in a stress-free “shear zone” in the vicinity of the fault zone. The bottom displacement represents the regional relative plate motion. Results show that the basin deformation depends critically on the width of the shear zone and on the amount of overlap between basin-bounding faults. As the width of the shear zone increases, the depth of the basin decreases, the rotation around a vertical axis near the fault tips decreases, and the basin shape (the distribution of subsidence normalized by the maximum subsidence) becomes broader. In contrast, two-dimensional plane stress modeling predicts a basin shape that is independent of the width of the shear zone. Our models also predict full-graben profiles within the overlapped region between bounding faults and half-graben shapes elsewhere. Increasing overlap also decreases uplift near the fault tips and rotation of blocks within the basin. We suggest that the observed structure of the Dead Sea Basin can be described by a 3-D model having a large overlap (more than 30 km) that probably increased as the basin evolved as a result of a stable shear motion that was distributed laterally over 20 to 40 km.