<p><b>Background</b>Aerobic exercise training (AET) prescribed as lipid management treatment positively affects the standard lipid profile and reduces cardiovascular disease (CVD) risk. Apolipoproteins, lipid and apolipoprotein ratios, and lipoprotein sub-fractions may more effectively predict CVD risk than the standard lipid profile but an AET response in these biomarkers has not been established.</p><p><b>Objectives</b> We conducted a quantitative systematic review of randomised controlled trials (RCTs) to (1) determine the effects of AET on lipoprotein sub-fractions, apolipoproteins and relevant ratios; and (2) identify study or intervention covariates associated with change in these biomarkers.</p><p><b>Methods</b> We searched PubMed, EMBASE, all Web of Science and EBSCO health and medical online databases from inception to 31 December 2021. We included published RCTs of adult humans with ≥ 10 per group of participants; an AET intervention duration ≥ 12 weeks of at least moderate intensity (> 40% maximum oxygen consumption); and reporting pre/post measurements. Non-sedentary subjects, or those with chronic disease other than Metabolic Syndrome factors, or pregnant/lactating, as well as trials testing diet/medications, or resistance/isometric/unconventional training interventions, were excluded.</p><p><b>Results</b> Fifty-seven RCTs totalling 3194 participants were analysed. Multivariate meta-analysis showed AET significantly raised antiatherogenic apolipoproteins and lipoprotein sub-fractions (mmol/L mean difference (MD) 0.047 (95% confidence interval (CI) 0.011, 0.082), P=.01); lowered atherogenic apoliproteins and lipoprotein sub-fractions (mmol/L MD − 0.08 (95% CI − 0.161, 0.0003), P=.05); and improved atherogenic lipid ratios (MD − 0.201 (95% CI − 0.291, − 0.111), P<.0001). Multivariate meta-regression showed intervention variables contributed to change in lipid, sub-fraction, and apoliprotein ratios.</p><p><b>Conclusion</b> Aerobic exercise training positively impacts atherogenic lipid and apolipoprotein ratios, alipoproteins, and lipoprotein sub-fractions; and antiatherogenic apolipoproteins and lipoprotein sub-fractions. Cardiovascular disease risk predicted by these biomarkers may be lowered when AET is prescribed as treatment or prevention.</p>