Despite high tuberculosis (TB) treatment success rate, treatment adherence is one of the major obstacles to tuberculosis control in Kenya. Our objective was to identify patient-related factors that were associated with time to TB treatment interruption and the geographic distribution of the risk of treatment interruption by county. Data of new and retreatment patients registered in TIBU, a Kenyan national case-based electronic data recording system, between 2013 and 2014 was obtained. Kaplan-Meier curves and log rank tests were used to assess the adherence patterns. Mixed-effects Cox proportional hazards modeling was used for multivariate analysis. Records from 90,170 patients were included in the study. The cumulative incidence of treatment interruption was 4.5% for new patients, and 8.5% for retreatment patients. The risk of treatment interruption was highest during the intensive phase of treatment. Having previously been lost to follow-up was the greatest independent risk factor for treatment interruption (HR: 4.79 [3.99, 5.75]), followed by being HIV-positive not on ART (HR: 1.96 [1.70, 2.26]) and TB relapse (HR: 1.70 [1.44, 2.00]). Male and underweight patients had high risks of treatment interruption (HR: 1.46 [1.35, 1.58]; 1.11 [1.03, 1.20], respectively). High rates of treatment interruption were observed in counties in the central part of Kenya while counties in the northeast had the lowest risk of treatment interruption. A better understanding of treatment interruption risk factors is necessary to improve adherence to treatment. Interventions should focus on patients during the intensive phase, patients who have previously been lost to follow-up, and promotion of integrated TB and HIV services among public and private facilities.