Background This study aimed to investigate whether the addition of visceral manipulation, to a standard physiotherapy algorithm, improved outcomes in patients with low back pain. Methods Sixty-four patients with low back pain who presented for treatment at a private physiotherapy clinic were randomized to one of two groups: standard physiotherapy plus visceral manipulation (n = 32) or standard physiotherapy plus placebo visceral manipulation (n = 32). The primary outcome was pain (measured with the 0-10 Numerical Pain Rating Scale) at 6 weeks. Secondary outcomes were pain at 2 and 52 weeks, disability (measured with the Roland-Morris Disability Questionnaire) at 2, 6 and 52 weeks and function (measured with the Patient-Specific Functional Scale) at 2, 6 and 52 weeks. This trial was registered with the Australia and New Zealand Clinical Trials Registry (ACTRN12611000757910). Results The addition of visceral manipulation did not affect the primary outcome of pain at 6 weeks (-0.12, 95% CI = -1.45 to 1.21). There were no significant between-group differences for the secondary outcomes of pain at 2 weeks or disability and function at 2, 6 or 52 weeks. The group receiving addition of visceral manipulation had less pain than the placebo group at 52 weeks (mean 1.57, 95% CI = 0.32 to 2.82). Participants were adequately blinded to group status and there were no adverse effects reported in either group. Conclusions Our study suggests that visceral manipulation in addition to standard care is not effective in changing short-term outcomes but may produce clinically worthwhile improvements in pain at 1 year.