Background Foods provided in childcare services are not consistent with dietary guideline recommendations. Web-based systems offer unique opportunities to support the implementation of such guidelines. Objective This study aimed to assess the effectiveness of a Web-based menu planning intervention in increasing the mean number of food groups on childcare service menus that comply with dietary guidelines. Secondary aims were to assess the impact of the intervention on the proportion of service menus compliant with recommendations for (1) all food groups; (2) individual food groups; and (3) mean servings of individual food groups. Childcare service use and acceptability of the Web-based program were also assessed. Methods A single-blind, parallel-group randomized controlled trial was undertaken with 54 childcare services in New South Wales, Australia. Services were randomized to a 12-month intervention or usual care control. Intervention services received access to a Web-based menu planning program linked to their usual childcare management software system. Childcare service compliance with dietary guidelines and servings of food groups were assessed at baseline, 3-month follow-up, and 12-month follow-up. Results No significant differences in the mean number of food groups compliant with dietary guidelines and the proportion of service menus compliant with recommendations for all food groups, or for individual food groups, were found at 3- or 12-month follow-up between the intervention and control groups. Intervention service menus provided significantly more servings of fruit (P<.001), vegetables (P=.03), dairy (P=.03), and meat (P=.003), and reduced their servings of discretionary foods (P=.02) compared with control group at 3 months. This difference was maintained for fruit (P=.03) and discretionary foods (P=.003) at 12 months. Intervention childcare service staff logged into the Web-based program an average of 40.4 (SD 31.8) times and rated the program as highly acceptable. Conclusions Although improvements in childcare service overall menu and individual food group compliance with dietary guidelines were not statistically significant, findings indicate that a Web-based menu planning intervention can improve the servings for some healthy food groups and reduce the provision of discretionary foods. Future research exploring the effectiveness of differing strategies in improving the implementation of dietary guidelines in childcare services is warranted. Trial Registration Australian New Zealand Clinical Trial Registry (ANZCTR): 16000974404; http://www.anzctr.org.au/ACTRN12616000974404.aspx