The extent of ambulatory recovery after motor incomplete spinal cord injury (miSCI) differs considerably amongst affected persons. This makes individual outcome prediction difficult and leads to increased within-group variation in clinical trials. The aim of this study on subjects with miSCI was (1) to rank the strongest single predictors and predictor combinations of later walking capacity, (2) to develop a reliable algorithm for clinical prediction, and (3) to identify subgroups with only limited recovery of walking function. Correlation and logistic regression analyses were performed on a dataset of 90 subjects, with tetra- or paraparesis, recruited in a prospective European multicenter study. Eleven measures obtained in the subacute injury period, including clinical examination, tibial somato-sensory evoked potentials (tSSEP) and demographic factors, were related to ambulatory outcome (WISCI II, 6minWT) 6 months after injury. The lower extremity motor score (LEMS) alone and in combination was identified as most predictive for later walking capacity in miSCI. Ambulatory outcome of subjects with tetraparesis was correctly predicted for 92% (WISCI II) or 100% (6minWT) of the cases when LEMS was combined with either tSSEP or the ASIA Impairment Scale, respectively. For individuals with paraparesis, prediction was less distinct mainly due to low prediction rates for individuals with poor walking outcome. A clinical algorithm was generated that allowed for the identification of a subgroup composed of individuals with tetraparesis and poor ambulatory recovery. These data provide evidence that a combination of predictors enables a reliable prediction of walking function and early patient stratification for clinical trials in miSCI.