The aim of Part II of this two-part study is to describe and analyze the association of various aspects and measurements related to the morphometry of the skull and craniocervical region to CM/SM status of Pomeranians, by means of computed tomography (CT) and magnetic resonance imaging (MRI). Prospectively, Pomeranians were included that underwent both CT and MRI studies of the head and cervicothoracic vertebral column. For those cases where qualitative classifications differed between observers, the experienced observer re-evaluated the studies and decided on a final classification that was used for further analysis. For quantitative measurements, the means of the observers' measurements were used for analysis. Among statistically significant differences in measurements, we found that dogs with SM had a significantly shorter clivus length based on both MRI (p = 0.01) and CT measurements (p = 0.01), and a significantly smaller caudal cranial fossa area based on both MRI (p = 0.02) and CT measurements (p = 0.02). Significant morphometrical differences were identified between dogs with or without CM/SM. The findings in this study add to those already described in other breeds and provide further insight into factors that may play a role in the pathogenesis of CM/SM in Pomeranians.