Abstract Objectives To obtain comprehensive insight into the association of ciprofloxacin use at different times in the past with the current risk of detecting resistance. Methods This retrospective nested case–control study of ciprofloxacin users used Dutch data from the PHARMO Database Network and one laboratory for the period 2003–14. Cases and controls were selected as patients with an antibiotic susceptibility test (AST) indicating ciprofloxacin resistance or susceptibility, respectively. We performed univariable and multivariable conditional logistic regression analyses, defining time-dependent exposure using standard definitions (current ciprofloxacin use, used 0–30, 31–90, 91–180 and 181–360 days ago) and a flexible weighted cumulative effect (WCE) model with four alternative time windows of past doses (0–30, 0–90, 0–180 and 0–360 days). Results The study population consisted of 230 cases and 909 controls. Under the standard exposure definitions, the association of ciprofloxacin use with resistance decreased with time [current use: adjusted OR 6.8 (95% CI 3.6–12.4); used 181–360 days ago: 1.3 (0.8–1.9)]. Under the 90 day WCE model (best-fitting model), more recent doses were more strongly associated with resistance than past doses, as was longer or repeated treatment. The 180 day WCE model, which fitted the data equally well, suggested that doses taken 91–180 days ago were also significantly associated with resistance. Conclusions The estimates for the association between ciprofloxacin use at different times and resistance show that ciprofloxacin prescribers should consider ciprofloxacin use 0–180 days ago to ensure that patients receive suitable treatment. The OR of ciprofloxacin resistance could be reduced by eliminating repeated ciprofloxacin prescription within 180 days and by treating for no longer than necessary.