Abstract  Amyotrophic lateral sclerosis is a progressive neurodegenerative disease that targets some somatic motoneuron populations, while others, e.g. those of the oculomotor system, are spared. The pathophysiological basis of this pattern of differential vulnerability, which is preserved in a transgenic mouse model of amyotrophic lateral sclerosis (SOD1^G93A), and the mechanism of neurodegeneration in general are unknown. Hyperexcitability and calcium dysregulation have been proposed by others on the basis of data from juvenile mice that are, however, asymptomatic. No studies have been done with symptomatic mice following disease progression to the disease endstage. Here, we developed a new brainstem slice preparation for whole‐cell patch‐clamp recordings and single cell fura‐2 calcium imaging to study motoneurons in adult wild‐type and SOD1^G93A mice up to disease endstage. We analysed disease‐stage‐dependent electrophysiological properties and intracellular Ca²⁺ handling of vulnerable hypoglossal motoneurons in comparison to resistant oculomotor neurons. Thereby, we identified a transient hyperexcitability in presymptomatic but not in endstage vulnerable motoneurons. Additionally, we revealed a remodelling of intracellular Ca²⁺ clearance within vulnerable but not resistant motoneurons at disease endstage characterised by a reduction of uniporter‐dependent mitochondrial Ca²⁺ uptake and enhanced Ca²⁺ extrusion across the plasma membrane. Our study challenged the notion that hyperexcitability is a direct cause of neurodegeneration in SOD1^G93A mice, but molecularly identified a Ca²⁺ clearance deficit in motoneurons and an adaptive Ca²⁺ handling strategy that might be targeted by future therapeutic strategies.