Branchiosaurids are small Permo-Carboniferous temnospondyls that retained an immature morphology and external gills throughout ontogeny. Their preservation of numerous size classes makes them outstanding examples for the study of ontogenetic patterns. Here, ontogenetic data of several branchiosaurids are analyzed in order to reconstruct and compare developmental trajectories. These trajectories are based on numerical changes, marked by the successive appearance of bones in the skeleton. The earliest phases in the formation of the skull are preserved only in two species, Apateon caducus and Melanerpeton humbergense. Despite being distant relatives within the clade, their ontogenetic trajectories are similar in the early formation of dentigerous elements in the jaws and palate, and a slower development of the median skull roof as compared with the smaller branchiosaurids Apateon pedestris, A. gracilis, and A. dracyi. Patterns shared by all five species are (1) the late formation and slow completion of circumorbital elements and most details of their temporal succession, (2) an anteroposterior progression of ossification in the postcranium, and (3) a delayed appearance of the interclavicle with respect to outgroups. In addition, Melanerpeton humbergense and Apateon caducus share the earlier appearance of the humerus relative to the femur. Apart from differences in growth rates of single elements, the analyzed trajectories differ in the chronological order of bone formation. These discrepancies are largely restricted to the late phase of larval development, and they affect the formation of the hyobranchial apparatus, sclerotic ring, scapula, and the last dermal bones to appear in the skull roof (postfrontal, postorbital, tabular, and jugal). The observed variation is probably a result of disassociated heterochrony, which is supported by comparison with outgroups such as Sclerocephalus.