Abstract Background Spinal adhesive arachnoiditis is a chronic inflammatory process of the leptomeninges and intrathecal neural elements. The possible causes of arachnoiditis are: infections, injuries of spinal cord, surgical procedures and intrathecal administration of therapeutic substances or contrast. Case presentation We present a case of 56-old woman with spinal muscular atrophy type 3 who developed a severe back pain in the lumbosacral region after the fifth dose of nusinersen given intrathecally. Magnetic resonance of lumbosacral spine showed spinal adhesive arachnoiditis. She received high doses of methylprednisolone intravenously, and later non-steroidal anti-inflammatory drugs, alpha lipoic acid, vitamins and rehabilitation with slight improvement. Conclusions The authors summarize that scheduled resonance imaging of the lumbosacral spine may be an important element of the algorithm in the monitoring of novel, intrathecal therapy in patients with spinal muscular atrophy.