Urinary retention is a serious complication of spinal cord injury. This study examined whether repetitive functional magnetic stimulation (rFMS) applied over the sacral nerve root affected bladder function or mood in patients with urinary retention after spinal cord injury. This single-center, case-control study included 32 patients with detrusor flaccid neurogenic bladder after spinal cord injury, who were randomly assigned to rFMS (n = 11), electroacupuncture pudinal nerve stimulation (EAPNS; n = 11), and control groups (n = 10). All groups received routine bladder function training. The S3 sacral nerve was stimulated at a frequency of 5 Hz, once per day for 4 consecutive weeks in the rFMS group. Electroacupuncture stimulation of the pudendal nerve was performed once daily for 4 weeks in the EAPNS group. The control group received bladder function retraining alone. After the 4-week treatment, there were significant improvements in all three groups (P < 0.05). Primary bladder sensation, maximum bladder volume, maximum bladder pressure, and residual urine were significantly higher in the rFMS group than in the other two groups (P < 0.05). Primary bladder sensation, maximum bladder volume, residual urine, and urinary leukocyte count were significantly different between the EAPNS and control groups (P < 0.05). The rFMS group had significantly lower scores in the self-rated anxiety scale and self-rated depression scale compared with those of the other two groups. The quality of life score significantly increased in all three groups. rFMS is conducive to the recovery of neurogenic function in patients with urinary retention. This study provides a scientific basis for the clinical application and promotion of rFMS.