A prospective, multicenter, randomized, open-label, controlled clinical trial was performed to evaluate the effectiveness and safety of the homeopathic product ZinCyp-3-02 in children with sleep disorders for ≥ one month compared to glycine. Children ≤ six years old received either ZinCyp-3-02 (N = 89) or comparator glycine (N = 90). After treatment for 28 days, total sleep-disorder-associated complaints severity scores decreased in both groups from median 7.0 (out of maximum 11.0) points to 2.0 (ZinCyp-3-02) and 4.0 (glycine) points, respectively, with overall higher odds of showing improvement for ZinCyp-3-02 (odds ratio: 4.45 (95% CI: 2.77-7.14), p < 0.0001, POM overall treatment related effect). Absence of individual complaints (time to sleep onset, difficulties maintaining sleep, sleep duration, troubled sleep (somniloquism), physical inactivity after awakening, restlessness for unknown reason, and sleep disorders frequency) at study end were significantly higher with ZinCyp-3-02 (all p values < 0.05). More children with ZinCyp-3-02 were totally free of complaints (p = 0.0258). Treatment effectiveness (p < 0.0001) and satisfaction assessments (p < 0.0001) were more favorable for ZinCyp-3-02. Few nonserious adverse drug reactions were reported (ZinCyp-3-02: N = 2, glycine: N = 1) and both treatments were well tolerated. Treatment with the homeopathic product ZinCyp-3-02 was found to be safe and superior to the comparator glycine in the treatment of sleep disorders in children.