Crustal deformation and seismicity in the Levant region are mainly related to the plate-boundary Dead Sea Fault (DSF) and the intraplate Carmel–Gilboa–Faria Fault System (CGFS). The intersection between these two major fault systems is generally treated as an ∼35-km-wide deformation belt stretched between the Faria and Gilboa Faults. Here, we present spatial and temporal analysis of faulting near this intersection. Our analysis is based on new geological mapping, new high-resolution airborne light detection and ranging (LiDAR) data, and seismic reflection profiles and indicates northward migration and localization of the intersection over time since the early Miocene. We discovered and mapped outcrops of Miocene, Pliocene, and Pleistocene rock units as well as faults and reconstructed the evolution of deformation. Three main tectonic phases were identified in this area covering the following periods: the early–middle Miocene, the late Miocene–Pliocene, and the Quaternary. During the first phase, the DSF and the CGFS developed, and the CGFS faulted along a series of subparallel grabens and elongated NW–SE, between the southernmost Faria and the northernmost Gilboa faults, over a belt width of ∼35 km. During the second phase, deformation along the CGFS migrated northward and concentrated at an ∼6-km-wide zone in the northern Faria Anticline. During the third stage, small-scale northward migration and localization of the deformation to a width zone of ∼1–2 km at the southern boundary of the Beit She’an Valley occurred. Faults from the third phase reveal both sinistral and normal faulting. We propose that the currently active intersection between the DSF and the CGFS is located east of this localized deformation zone, near a right step of the DSF and the uplifted area of Tel Al-Qarn in the eastern Jordan Valley. We suggest that the northward migration and localization of this intersection are related to regional tectonic changes, spatial variations in the Sinai-Arabia Euler pole, and the localization of deformation along the DSF.