Sensorimotor cortical activity is altered in both the immediate acute, and chronic stages of musculoskeletal pain. However, these changes are opposite, with decreased cortical activity reported in experimentally-induced acute pain (lasting minutes to hours), and increased cortical activity in chronic, clinical pain (lasting>6 months). It is unknown whether sensorimotor cortical activity is altered in acute, clinical musculoskeletal pain (lasting<4 weeks). In 36 individuals with acute, non-specific, clinical low back pain (LBP) and 36 age- and sex-matched, pain-free controls, we investigated the processing of non-noxious afferent inputs using sensory evoked potentials (SEPs), as well as corticomotor excitability and organisation of the primary motor cortex using transcranial magnetic stimulation. Processing of non-noxious sensory inputs was lower (smaller area of the N-N-P SEP complex) in acute LBP (F=45.28, p<0.01). Examination of specific SEP components revealed smaller area of the N and P SEP components in acute LBP, although inter-individual variability was high. Motor cortical map volume was lower in acute LBP (F=5.61, p=0.02). These findings demonstrate that acute LBP is characterised by lower sensorimotor cortical activity at the group level. However, individual variation was high, suggesting individual adaptation of cortical plasticity in acute pain. Perspective: This is the first study to examine sensorimotor cortical activity in the acute stage of clinical low back pain. This information is critical for understanding the neurophysiology of acute low back pain.