Objective. To assess the uptake of isoniazid preventive therapy (IPT) by eligible children in Kigali, Rwanda, and associated individual, households, and healthcare systems characteristics. Methods. A cross-sectional study was conducted among child contacts of index cases having sputum smear-positive pulmonary tuberculosis. Data were collected from 13 selected primary health centres. Descriptive statistics were used to generate frequency tables and figures. Logistic regression models were performed to determine characteristics associated with IPT uptake. Results. Of 270 children (under 15 years), who were household contacts of 136 index cases, 94 (35%) children were less than 5 years old and eligible for IPT; and 84 (89%, 95% CI 81–94) were initiated on IPT. The reasons for not initiating IPT in the remaining 10 children were parents/caregivers’ lack of information on the need for IPT, refusal to give IPT to their children, and poor quality services offered at health centres. Factors associated with no uptake of IPT included children older than 3 years, unfriendly healthcare providers, HIV infected index cases, and the index case not being the child’s parent. Conclusion. The National Tuberculosis Program’s policy on IPT delivery was effectively implemented. Future interventions should find strategies to manage factors associated with IPT uptake.