Objective: To determine the independent predictors for clinician fatigue and decline in cognitive function following a shift in the ED during early stages of the COVID-19 pandemic. Methods: This was a prospective, quasi-experimental study conducted in a metropolitan adult tertiary-referral hospital ED over 20 weeks in 2021. The participants were ED doctors and nurses working clinical shifts in an ED isolation area or high-risk zone (HRZ) with stringent personal protective equipment (PPE). The participants' objective and subjective fatigue was measured by the Samn–Perelli fatigue score and a psychomotor vigilance ‘smart game’ score, respectively. Postural signs/symptoms and urine specific gravity (SG) were measured as markers of dehydration. Results: Sixty-three participants provided data for 263 shifts. Median (interquartile range) age was 33 (28–38) years, 73% were female. Worsening fatigue score was associated with working afternoon shifts (afternoon vs day, adjusted odds ratio [aOR] 5.16 [95% confidence interval (CI) 1.32–20.02]) and in non-HRZ locations (HRZ vs non-HRZ, aOR 0.23 [95% CI 0.06–0.87]). Worsening cognitive function (game score) was associated with new onset postural symptoms (new vs no symptoms, aOR 4.14 [95% CI 1.34–12.51]) and afternoon shifts (afternoon vs day, aOR 3.13 [95% CI 1.16–8.44]). Working in the HRZ was not associated with declining cognitive function. Thirty-four (37%) of the 92 participants had an end of shift urine SG >1.030. Conclusion: Working afternoon shifts was associated with fatigue. There was no association between HRZ allocation and fatigue, but our study was limited by a low COVID workload and fluctuating PPE requirements in the non-HRZs. Workplace interventions that target the prevention of fatigue in ED clinicians working afternoon shifts should be prioritised.