Background Despite the increasing demand for complementary and integrative medicine, only a few studies have evaluated the effect of these types of treatments on the quality of life (QoL) of patients with chronic diseases. The objective of this study was to evaluate the QoL of women treated with homeopathy within the Public Health System of Belo Horizonte, Brazil. Methods This is a prospective randomized controlled pragmatic trial. The patients were divided into two independent groups, one group underwent homeopathic treatment in the first 6-month period and the other did not receive any homeopathic treatment. In both randomized groups, patients maintained their conventional medical treatment when necessary. The World Health Organization Quality of Life abbreviated questionnaire (WHOQOL-BREF) was used for QoL analysis prior to treatment and 6 months later. Results Randomization afforded similar baseline results in three domains of QoL analysis for both groups. After 6 months’ treatment, there was a statistically significant difference between groups in the physical domain of WHOQOL-BREF: the average score improved to 63.6 ± (SD) 15.8 in the homeopathy group, compared with 53.1 ± (SD) 16.7 in the control group. Conclusions Homeopathic treatment showed a positive impact at 6 months on the QoL of women with chronic diseases. Further studies should be performed to determine the long-term effects of homeopathic treatment on QoL and its determinant factors.