Determine the incidence of loss to follow-up (LTFU) in patients treated for rifampicin-resistant tuberculosis (RR-TB) or multidrug-resistant tuberculosis (RR/MDR-TB), and the factors associated with this discharge status in Ecuador.Retrospective cohort study of patients with RR/MDR-TB who followed the World Health Organization's 18-24-month treatment regimen in 2014 and 2015, as reported by the Ministry of Health of Ecuador. The incidence of LTFU was determined, and clinical and epidemiological manifestations of cases discharged as LTFU were compared with those discharged as successfully treated. Survival was analyzed with Cox regression in order to evaluate factors associated with LTFU.Of 328 cases, 270 (82.3%) were analyzed because they had a reported discharge status. Discharge as LTFU accounted for 39.6% of cases, and as successfully treated, 50.4%. The risk factors associated with LTFU were: previous discharge as LTFU in a previous TB episode [hazard ratio (HR): 2.96 (1.53-5.73), < 0.001]; addiction to alcohol or drugs [HR: 2.82 (1.10-7.23), = 0.031]; and having an Xpert diagnosis (TB-RR) [HR: 1.53 (1.0-2.35), = 0.048]. Of the total LTFU, 43% occurred after nine months of treatment.The incidence of LTFU in patients with RR/MDR-TB in Ecuador is above the average for the Region of the Americas. The three identified factors support implementation of shorter regimens and patient-centered care, in line with the End TB Strategy.