Spinal muscular atrophy (SMA) is an autosomal recessive disorder caused by the deletion or/and mutation in the survival motor neuron 1 (SMN1) gene on chromosome 5. Until now, only a few articles investigating the relationship between upper limb function and the gross motor function in untreated SMA patients have been published. However, there is still a lack of publications including the relationship between structural changes such as cervical rotation, trunk rotation and side trunk shortening, and upper limb function. The aim of the study was to examine the upper limb function in patients with spinal muscular atrophy and the relationship between the upper limb function, gross motor function, and structural parameters. We present an analysis of 25 SMA patients, divided into sitter and walker groups, undergoing pharmacological treatment (nusinersen or risdiplam), examined twice between the initial examination and evaluation after a 12-month period. The participants were tested using validated scales such as the Revised Upper Limb Module (RULM), the Hammersmith Functional Motor Scale—Extended (HFMSE), and the structural parameters. Our results showed that patients demonstrated greater improvement on the RULM scale than on the HFMSE scale. Moreover, persistent structural changes negatively affected both the upper limb function and gross motor skills.