The structure of the Neogene–Quaternary Ptolemais sedimentary basin exemplifies the importance of deformation partitioning in the kinematic history of basin formation. Structural analyses were carried out at outcrop from the metre to kilometre scale on basin marginal faults, and on structures reflecting deformation of the interior of the basin. Deformation is partitioned into three spatially separated, but kinematically linked domains. Two transtensional-dominated domains in the northern and in the southern parts are separated by a transpressional-dominated domain in the central part of the basin. Intense synsedimentary deformation of Pliocene–Quaternary deposits occurred in all three domains. Dominant structures that affected pre-Neogene lithologies and the basin-fill include (E)NE–(W)SW- and NW–SE-trending basin kilometre-scale marginal faults. We propose that the structures of the three domains were active simultaneously during progressive deformation reflecting an overall transtensional-dominated regime. The deformation is imposed by boundary conditions and is consistent with the Pliocene–Quaternary large-scale deformation in northern Greece that includes clockwise (dextral) rotations of crustal blocks and gravity-driven NNW–SSE extension. Strong partitioning of deformation produced contrasting structures, which do not reflect a sequence of events related to a regional stress fields that changed with time.