Schoolchildren are commonly linked to influenza transmission. Handwashing with soap has been shown to decrease infections; however, improving handwashing practices using soap and water is difficult in low-resource settings. In these settings, alternative hygiene options, such as hand sanitizer, could improve handwashing promotion to reduce influenza virus infections. We conducted a cluster randomized control trial in 24 primary schools in Dhaka to assess the effectiveness of hand sanitizer and a respiratory hygiene education intervention in reducing influenza-like illness (ILI) and laboratory-confirmed influenza during June-September 2015. Twelve schools were randomly selected to receive hand sanitizer and respiratory hygiene education, and 12 schools received no intervention. Field staff actively followed children daily to monitor for new ILI episodes (cough with fever) through school visits and by phone if a child was absent. When an illness episode was identified, medical technologists collected nasal swabs to test for influenza viruses. During the 10-week follow-up period, the incidence of ILI per 1,000 student-weeks was 22 in the intervention group versus 27 in the control group (P-value = 0.4). The incidence of laboratory-confirmed influenza was 53% lower in the intervention schools (3/1,000 person-weeks) than in the control schools (6/1,000 person-weeks) (P-value = 0.01). Hand sanitizer and respiratory hygiene education can help to reduce the risk of influenza virus transmission in schools.