BackgroundTime‐varying drug treatments are common in studies using routinely collected health data (RCD) for assessing treatment effects. This study aimed to examine how these studies reported, handled, and interpreted time‐varying drug treatments.MethodsA systematic search was conducted on PubMed from 2018 to 2020. Eligible studies were those used RCD to explore drug treatment effects. We summarized the reporting characteristics and methods employed for handling time‐varying treatments. Logistic regressions were performed to investigate the association between study characteristics and the reporting of time‐varying treatments.ResultsTwo hundred and fifty‐six studies were included, and 225 (87.9%) studies involved time‐varying treatments. Of these, 24 (10.7%) reported the proportion of time‐varying treatments and 105 (46.7%) reported methods used to handle time‐varying treatments. Multivariable logistic regression showed that medical studies, prespecified protocol, and involvement of methodologists were associated with a higher likelihood of reporting the methods applied to handle time‐varying treatments. Among the 105 studies that reported methods, as‐treated analyses were the most commonly used analysis sets, which were employed in 73.9%, 75.3% and 88.2% of studies that reported approaches for treatment discontinuation, treatment switching and treatment add‐on. Among the 225 studies involved time‐varying treatments, 27 (12.0%) acknowledged the potential bias introduced by treatment change, of which 14 (51.9%) suggested that potential biases may impact acceptance or rejection of the null hypothesis.ConclusionsAmong observational studies using RCD, the underreporting about the presence and methods for handling time‐varying treatments was largely common. The potential biases due to time‐varying treatments have frequently been disregarded. Collaborative endeavors are strongly needed to enhance the prevailing practices.