Background Hypercholesterolaemia and physical inactivity significantly contribute towards risk of coronary heart disease. Increased physical activity may be an effective way to improve lipid profiles in hypercholesterolaemic individuals. The aim of this study was to investigate whether a home-based physical activity program meeting current guidelines improved the lipid profile of hypercholesterolaemic men. Methods Sixty-seven hypercholesterolaemic men (55.1 (4.9) years), from Bristol England, recruited between 2002–2004, were randomized to either 12 weeks of brisk walking sufficient to expend at least 300 kcal each walk or control condition. Fasting lipids including total cholesterol (TC), high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C), triglycerides (TG), glucose, insulin, blood pressure and anthropometric characteristics were measured at baseline and follow-up. Compliance was monitored using accelerometers and activity logs. Results After controlling for baseline differences, TC/HDL-C was significantly lower in the intervention group at follow-up (− 0.28, 95% CI: − 0.52, − 0.03, p = 0.03). An increase in HDL-C (0.07 mmol/l: − 0.01, 0.12, p = 0.07) and reduction in TG (− 0.30 mmol/l: − 0.64, 0.03, p = 0.07) in intervention participants were of borderline statistical significance. Weight significantly decreased in intervention participants (− 1.40 kg: − 2.43, − 0.38, p < 0.01). No other significant between group effects were found. Compliance to the walking program was 97.6%. Conclusions Twelve weeks of moderate intensity walking was sufficient to improve TC/HDL-C in hypercholesterolaemic men, primarily through improvement in HDL-C.