Background and objectives People with posttraumatic stress disorder (PTSD) may experience heightened stress reactivity. Eye Movement Desensitization and Reprocessing (EMDR) is an evidence-based treatment involving eye movements while retrieving memories. We evaluated if EMD participants had less stress reactivity than retrieval-only participants after personal trauma scripts. We also investigated changes in daily cortisol levels related to treatment outcomes. Methodology PTSD participants (N = 91) were randomly assigned to EMD (N = 47) or retrieval-only conditions (N = 44). Baseline and post-treatment data were collected and measured using Heart rate variability (HRV), heart rate (HR), pre-ejection period (PEP), and cortisol levels (AUC; the area under the curve, and CAR; the cortisol awakening response). We conducted a linear mixed model to analyze the main outcomes. Results No difference between EMD and retrieval-only in the reduction of stress reactivity and acceleration of recovery over time. Both groups showed that HR and PEP reactivity to the trauma script decreased significantly after treatment. In contrast, only EMD group experienced an acceleration of HR recovery in response to trauma scripts following treatment. Cortisol measures showed an inconsistent pattern, with a higher CAR in retrieval-only after treatment compared to EMD. However, no significant difference was found between groups in terms of AUC levels after treatment. Limitation The precision of measuring and analyzing saliva samples is highly dependent on the participant’s adherence to the schedule. Conclusion No specific benefits for eye movements was found in the current study. Both EMDR and retrieval-only can reduce stress reactivity in treating PTSD. Clinical Trial Registration [www.ClinicalTrials.gov], identifier [ISRCTN55239132].