Purpose The aim of this study was to characterize the the effects of clonidine on sedation, heart rate (HR) and mean arterial blood pressure (MAP) in critically ill, mechanically ventilated adult patients, using population pharmacodynamic modelling. Methods Thirty-two patients received continuous intravenous clonidine, added to standard sedation, at 0, 600, 1200 or 1800 μg/day. Sedation, HR, and MAP were modelled as a function of predicted clonidine concentrations using NONMEM. Model performance was assessed by goodness-of-fit plots, bootstrapping, and visual predictive checks. Results The sedation model included 773 Richmond Agitation-Sedation scale (RASS) assessments with corresponding predicted clonidine concentrations. The probability of deep sedation (RASS ≤-4) was described by a logistic regression model with an intercept of 2.23 (relative standard error (RSE) 25%), slope of -0.383 (RSE 17%), and covariate effects of midazolam (-2.48, RSE 7%) and propofol (-1.54, RSE 13%). The hemodynamic models included 783 paired HR and MAP measurements. HR was best described by a linear model with a baseline of 90.6 bpm (RSE 2%) and slope of -3.30 bpm per µg/L (RSE 10%). MAP was also modelled linearly, with a baseline of 76.9 mmHg (RSE 2%), and slope of -0.887 mmHg per µg/L (RSE 42%). Including inter-individual variability on baseline values significantly improved both models. Conclusion In mechanically ventilated ICU patients, clonidine was associated with a dose-dependent increase in the probability of deep sedation, and with linear, dose-dependent reductions in HR and MAP.