In amyotrophic lateral sclerosis (ALS) motor cortex hyperexcitability is detected in both familial and sporadic cases, suggesting its centrality in the ALS phenotype; the underlying mechanisms, however, remain largely obscure. Here we utilize male and female UCHL1-eGFP (UeGFP) mice, in which the corticospinal neurons of the motor cortex are labeled with green fluorescent protein, to investigate the intrinsic excitability and synaptic inhibitory inputs on distinct neuron populations in WT-UeGFP and presymptomatic AlsinKO-UeGFP mice, which lack Alsin function and are a well-characterized mouse model for juvenile cases of ALS. We show that in the motor cortex of AlsinKO-UeGFP mice, eGFP-positive layer 5 pyramidal neurons, which represent upper motor neurons, show a decrease in intrinsic excitability compared with WT, whereas the electrophysiological properties of eGFP-negative cells, which identify callosal projection neurons, are unaffected. This alteration in intrinsic excitability, however, is counterbalanced by a decrease in the frequency of spontaneous inhibitory currents due to a cell-specific reduction in the number of inhibitory synaptic contacts on upper motor neurons. Thus, the overall excitability of upper motor neurons only displays negligible changes despite large alterations in intrinsic excitability and inhibitory synaptic input, which may explain why mice do not exhibit a prominent motor phenotype. The presence of this homeostatic interaction between intrinsic excitability and synaptic inhibition raises the question of which of the two changes is primary, and which is secondary, and shows that decreased function of motor cortex interneurons is an early event in ALS with Alsin mutations. Significance Statement We found that in AlsinKO mice, which recapitulate ALS disease in patients with Alsin mutations, intrinsic excitability and inhibitory synaptic input of upper motoneurons (but not callosal-projection neurons) are significantly reduced at presymptomatic disease stage. We show that in this model: 1) impaired function of cortical interneurons is an early event; 2) excitability alteration in the motor cortex is cell type-specific; 3) intrinsic excitability and synaptic inhibition are linked by a homeostatic mechanism. These results stress the importance of cortical interneurons in ALS and suggest that either homeostatic overcompensation or failure of compensation contribute to disease onset and progression. If these mechanisms are common in ALS patients, this may have important consequences for the design of novel therapeutic interventions.