This paper aims to simulate the kinematic evolution of a regional transect crossing the Northern Emirates in the northernmost part of the Semail Ophiolite and the Dibba zone, just south of the Musandam Platform exposures. The studied section comprises, from top to bottom and from inner to outer zones, (1) the erosional remnants of the Semail Ophiolite, mainly made up of serpentinized ultramafics in the west and gabbros in the east, (2) high-grade metamorphic rocks which are currently exposed in the core of a nappe anticline near Masafi, (3) far-travelled Hawasina basinal units and Sumeini paleo-slope units of the Dibba Zone, (4) parautochthonous platform carbonates, which are currently well exposed in the Musandam area, and (5) a flexural basin filled with uppermost Cretaceous to Neogene sediments. Two main compressional episodes are generally identified, resulting first in the obduction of the Semail Ophiolite and then in the stacking of underlying platform carbonate units of the former Arabian passive margin, thus accounting for the present architecture of this transect: (1) first, deformation at the plate boundary initiated in the Late Cretaceous, resulting in the obduction of the Semail Ophiolite and the progressive accretion of the Hawasina and Sumeini tectonic wedge on top of the Arabian foreland, leading to a progressive bending of its lithosphere and development of a wide flexural basin; (2) compression resumed during the Neogene, leading to the tectonic stacking of the parautochthonous platform duplexes of Musandam and Margham trends, the development of out-of-sequence thrusts and triangle zones, refolding of the sole thrust of the former Late Cretaceous accretionary wedge and coeval normal (?) high-angle faulting along the contact between the Musandam and Dibba zones. However, seismic profiles and paleo-thermometers also help in identifying another erosional event at the boundary between the Paleogene Pabdeh and the Neogene Fars series. Evidenced by the local erosional truncation of the Pabdeh series in the vicinity of the frontal triangle zone (i.e. the inner part of the former Late Cretaceous foredeep), this Paleogene uplift/unroofing episode is tentatively interpreted here as an evidence for a continuum of compressional deformation lasting from the Late Cretaceous to the Middle Miocene although one may alternatively speculate that it was related to the detachment of the subducted slab. Although carbonate facies are usually not suitable for apatite fission track (AFT) studies, we were able to extract detrital apatites from quartz-bearing Triassic dolomites in the Musandam area. However, the yield and the quality were both poor and too few fission track lengths could be measured, making it difficult to interpret the meaning of the FT ages. The FT dates obtained in this study are therefore compared with those existing in the literature. Fortunately enough, for each sample, at least ten apatite crystals could be used for fission track dating, except for site 6 with only five datable apatite grains. The obtained apatite fission track dates between 28 and 13 Ma, much younger than the Triassic age of the series, are taken to represent reset fission track ages, implying erosion of an up-to-3-km-thick pile of Jurassic–Cretaceous carbonates and Hawasina allochthon during the Neogene. Apatite fission track dates from the ~95 M-old plagiogranites of the Semail complex (Searle and Cox, Geol Mag 139(3):241–255, 2002) obtained in this study and compared with those recently published provide evidences for more than one cooling event. An early unroofing of the ophiolite during the Late Cretaceous is revealed in fission track dates of 72–76 Ma at the top of the ophiolite in the east, which are coeval and also consistent with the occurrence of paleo-soils, rudists and paleo-reefs on top of serpentinized ultramafics in the west. High-pressure rocks at As Sifah in the southeast near Muscat revealed apatite fission track data ranging from ~46 to 63 Ma (Gray et al. 2006). The leucocratic part of the ophiolite (sample UAE 180) yielded comparable young apatite (40.6 ± 3.9 Ma) and zircon (46.6 ± 4.3 Ma) FT dates. A Cenozoic (~20–21 Ma) exhumation has been determined for the Bani Hamid metamorphic sole in northern Oman, applying low temperature geochronology and combining apatite FT and apatite (U–Th)/He analyses (Gray et al. 2006). In this study, young apatite fission track dates of 20 Ma have also been found but at the base of the ophiolite near Masafi, in the core of the nappe anticline, thus indicating a Neogene age for the refolding of the allochthon and stacking of underlying parautochthonous platform carbonate units. During the subsequent 2D forward Thrustpack kinematic modelling of the regional transect, these AFT data-set has been used, together with available subsurface information, to reconstruct the past architecture of the structural sections through time, accounting for incremental deformation along the various decollement levels, synorogenic sedimentation and erosion, as well as for successive bending and unbending episodes of the Arabian lithosphere.