Background: Employing a rebaselining concept may reduce noise in retinal layer thinning measured by optical coherence tomography (OCT). Methods: From an ongoing prospective observational study, we included patients with relapsing multiple sclerosis (RMS), who had OCT scans at disease-modifying treatment (DMT) start (baseline), 6–12 months after baseline (rebaseline), and ⩾12 months after rebaseline. Mean annualized percent loss (aL) rates (%/year) were calculated both from baseline and rebaseline for peripapillary-retinal-nerve-fiber-layer (aLpRNFL_baseline/aLpRNFL_rebaseline) and macular-ganglion-cell-plus-inner-plexiform-layer (aLGCIPL_baseline/aLGCIPL_rebaseline) by mixed-effects linear regression models. Results: We included 173 RMS patients (mean age 31.7 years (SD 8.8), 72.8% female, median disease duration 15 months (12-94) median baseline-to-last-follow-up-interval 37 months (18-71); 56.6% moderately effective DMT (M-DMT), 43.4% highly effective DMT (HE-DMT)). Both mean aLpRNFL_baseline and aLGCIPL_baseline significantly increased in association with relapse (0.51% and 0.26% per relapse, p < 0.001, respectively) and disability worsening (1.10% and 0.48%, p < 0.001, respectively) before baseline, but not with DMT class. Contrarily, neither aLpRNFL_rebaseline nor aLGCIPL_rebaseline was dependent on relapse or disability worsening before baseline, while HE-DMT significantly lowered aLpRNFL_rebaseline (by 0.31%, p < 0.001) and aLGCIPL_rebaseline (0.25%, p < 0.001) compared with M-DMT. Conclusions: Applying a rebaselining concept significantly improves differentiation of DMT effects on retinal layer thinning by avoiding carry-over confounding from previous disease activity.