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Background: Adolescent girls' risk of school dropout and reproductive health (RH) challenges may be exacerbated by girls' attitudes toward their bodies and inability to manage their menstruation. We assessed effects of sanitary pad distribution and RH education on girls in primary grade 7 in Kilifi, Kenya. Methods: A cluster randomized controlled trial design was used. Eligible clusters were all non-boarding schools in three sub-counties in Kilifi County that had a minimum of 25 girls enrolled in primary grade 7. 140 primary schools, 35 per arm, were randomly assigned to one of four study arms: (1) control; (2) sanitary pad distribution; (3) RH education; or (4) both sanitary pad distribution and RH education. Outcomes were school attendance, school engagement, RH knowledge and attitudes, gender norms, and self-efficacy. For outcomes measured both at baseline and endline, difference-in-differences (DID) models were estimated and for outcomes without baseline data available, analysis of covariance models were used. Results: The study enrolled 3489 randomly selected girls in primary grade 7, with a mean age of 14.4 (SD 1.5). Girls in arms 2 and 4 received on average 17.6 out of 20 packets of sanitary pads and girls in arms 3 and 4 participated on average in 21 out of 25 RH sessions. Ninety-four percent of the baseline sample was interviewed at the end of the intervention with no differential attrition by arm. There was no evidence of an effect on primary school attendance on arm 2 (coefficient [coef] 0.37, 95% CI − 0.73, 1.46), arm 3 (coef 0.14, 95% CI − 0.99, 1.26) or arm 4 (coef 0.58, 95% CI −.37, 1.52). There was increased positive RH attitudes for girls in arm 3 (DID coef. 0.63, 95% CI 0.40–0.86) and arm 4 (DID coef. 0.85, 95% CI 0.64, − 1.07). There was also an increase in RH knowledge, gender norms and self-efficacy in arms 3 and 4. Conclusions: The findings suggest that neither sanitary pad distribution nor RH education, on their own or together, were sufficient to improve primary school attendance. However, as the RH education intervention improved RH outcomes, the evidence suggests that sanitary pad distribution and RH education can be positioned in broader RH programming for girls. Trial registration: ISRCTN, ISRCTN10894523. Registered 22 August 2017—Retrospectively registered, http://www.isrctn.com/ISRCTN10894523 Plain language summary: Adolescent girls face a range of challenges that may compromise their chances of completing school or their sexual and reproductive health. These challenges can be even further complicated by girls' feelings of shame about their bodies, in particular about menstruation, or their lack of sanitary products to help them manage menstruation. This study sought out to assess if providing girls in grade 7 in a rural, coastal area of Kenya with sanitary pads and sex education would alleviate some of those challenges. One hundred and forty schools were included in the study and 35 each were randomly assigned to one of the following program packages: (1) standard government provision of pads and health education; (2) regular monthly provision of sanitary pads; (3) sex education; or (4) both regular monthly provision of sanitary pads and sex education. The study found that none of the three program packages had an impact on school attendance, however those that participated in the sex education felt more positively about menstruation, knew more about sexual and reproductive health, had more equitable gender norms and were more self-confident at the end of the program. The study results show that addressing girls' menstrual health challenges are important, but are better positioned as part of comprehensive sexuality education programs addressing stigma and shame associated with menstruation, access to menstrual products, inequitable gender norms and sexual and reproductive health knowledge gaps, as opposed to a girls education intervention. [ABSTRACT FROM AUTHOR]