BackgroundLimited information is available about prognostic factors for recovery after spinal cord injury (SCI) to the L4‐S3 segments. Previous research suggests that L4‐S3 SCI does not have a worse prognosis than T3‐L3 SCI.Hypothesis/ObjectivesTo elucidate prognostic factors for regaining urinary continence and ambulation in dogs with L4‐S3 SCI and compare prognosis to T3‐L3 SCI.Animals/MethodsA retrospective study on 61 nonambulatory dogs with L4‐S3 SCI, matched to dogs with T3‐L3 SCI, compared 3 weeks after onset. Prognostic factors explored using logistic regression and used for matching: nonchondrodystrophic dogs >15 kg versus dogs that were chondrodystrophic or <15 kg; compressive versus noncompressive lesions; presence versus absence of conscious pain perception (CPP); and lower vs upper motor neuron (LMN/UMN) incontinence.ResultsFewer L4‐S3 dogs regained continence compared to T3‐L3 dogs (64 vs 85%, P = .0033), but no difference existed for regaining ambulation (66 vs 75%, P = .1306). In L4‐S3 SCI dogs, fewer dogs regained continence with loss of CPP (P < .001), LMN incontinence (P = .004), and noncompressive lesions (P = .006). Negative prognostic factors for regaining ambulation included absent CPP (P < .001) and large nonchondrodystrophic breed (P = .022).Conclusions and Clinical ImportanceDogs with L4‐S3 SCI have a poorer short‐term prognosis than do dogs with T3‐L3 SCI. Dogs with L4‐S3 SCI had a poor prognosis with loss of CPP, or noncompressive lesions combined with LMN incontinence. Small‐breed or chondrodystrophic dogs with retained CPP, compressive lesions, and UMN incontinence had an excellent prognosis. These findings may help guide decision‐making in L4‐S3 SCI.