Objective To evaluate improvement of stress urinary incontinence (SUI) and functional status of the urethra after autologous skeletal‐muscle derived cell (aSMDC) implantation. Methods Phase I–II, open, non‐randomized, single‐center study of ultrasound guided aSMDC implantation (dosed at 0.2 × 106 cells/2 mL) into the external urethral sphincter to treat SUI. Results A total of 38 patients were treated and followed for 2 years. SUI measured by Incontinence Episode Frequency score, short pad test, quality of life, patient's and clinician's perception significantly improved and remained improved after 2 years. However, urodynamic urethral properties in general did not improve at 1‐year after treatment. Subgroup analysis revealed that addition of an adjuvant functional electrical stimulation therapy discontinued 4 weeks after injection in the compliant group, gave better urodynamic values and maintained the long‐term SUI improvement at 2 years. Conclusion The aSMDC injection was safe and well‐tolerated by patients. The status of SUI improved and with it the quality of life of patients, even if this was not necessarily reflected in the urodynamic urethral properties. Electrical stimulation, as an adjuvant therapy, could have an essential role in the success of the therapy. Clinical registration Clinical study was registered under Eudra‐CT number: 2010‐021867‐34 at European Clinical Trial Database (EudraCT), accessible at: EudraCT (europa.eu). As SUI maintains improved 2 years after aSMDC injection, more in ES compliant group, functional urethral properties measured by urodynamics generally do not change.