The activities of neuronal populations exhibit temporal sequences that are thought to mediate spatial navigation, cognitive processing, and motor actions. The mechanisms underlying the generation and maintenance of sequential neuronal activity remain unclear. We found that layer 2 and/or 3 pyramidal neurons (PNs) showed sequential activation in the mouse primary motor cortex during motor skill learning. Concomitantly, the activity of somatostatin (SST)-expressing interneurons increased and decreased in a task-specific manner. Activating SST interneurons during motor training, either directly or via inhibiting vasoactive-intestinal-peptide-expressing interneurons, prevented learning-induced sequential activities of PNs and behavioral improvement. Conversely, inactivating SST interneurons during the learning of a new motor task reversed sequential activities and behavioral improvement that occurred during a previous task. Furthermore, the control of SST interneurons over sequential activation of PNs required CaMKII-dependent synaptic plasticity. These findings indicate that SST interneurons enable and maintain synaptic plasticity-dependent sequential activation of PNs during motor skill learning. •Sequential activity of pyramidal neurons emerges and stabilizes with motor training•SST interneurons regulate the establishment and stabilization of sequential activity•VIP interneurons regulate the establishment of sequential activity•The regulation of sequential activity involves CaMKII-dependent synaptic plasticity Adler et al. reveal mechanisms underlying learning-dependent sequential activation of pyramidal neurons in the primary motor cortex. SST-expressing interneurons and CaMKII-dependent synaptic plasticity control the establishment of sequential activity during motor training and prevent the interference from new learning.