This paper describes the protocol for a Phase I/II, parallel-group, blinded randomized controlled trial that compares the effects of 12-weeks of combined learning and memory rehabilitation with either aerobic cycling exercise or stretching on cognitive, neuroimaging, and everyday life outcomes in 60 persons with moderate-to-severe traumatic brain injury (TBI) who demonstrate impairments in new learning. Briefly, participants will undergo baseline testing consisting of neuropsychological testing, neuroimaging, daily life measures, and cardiorespiratory fitness. Following baseline testing, participants will be randomized to one of 2 conditions (30 participants per condition) using concealed allocation. Participants will be masked as to the intent of the conditions. The conditions will both involve supervised administration of an enhanced, 8-week version of the Kessler Foundation modified Story Memory Technique, embedded within either 12-weeks of supervised and progressive aerobic cycling exercise training (experimental condition) or 12-weeks of supervised stretching-and-toning (active control condition). Following the 12-week intervention period, participants will complete the same measures as at baseline that will be administered by treatment-blinded assessors. The primary study outcome is new learning and memory impairment based on California Verbal Learning Test (CVLT)-III slope, the secondary outcomes include neuroimaging measures of hippocampal volume, activation, and connectivity, and the tertiary outcomes involve measures of daily living along with other cognitive outcomes. We further will collect baseline sociodemographic data for examining predictors of response heterogeneity. If successful, this trial will provide the first Class I evidence supporting combined memory rehabilitation and aerobic cycling exercise training for treating TBI-related new learning and memory impairment.