Background: Pulmonary embolism (PE) is a potentially life-threatening condition. Although advances in diagnostic and risk-stratification tools have reduced acute mortality, few studies have evaluated its impact on quality of life after diagnosis. Aim: To assess health-related quality of life in patients with acute PE during hospitalization and three months after diagnosis using the PEmb-QoL questionnaire. Materials and Methods: This prospective longitudinal cohort study included 83 patients with acute PE who completed the PEmb-QoL questionnaire during hospitalization and at three-month follow-up. Six domains were assessed: symptom frequency, activities of daily living, work-related problems, social limitations, symptom intensity, and emotional complaints. Scores were transformed to a 0–100 scale, with higher scores indicating poorer quality of life. Statistical analyses were performed using SPSS 26.0. Paired scores were compared using the Wilcoxon signed rank test, and Spearman's correlation was used to assess associations with clinical severity indices. A linear mixed-effects model including PESI, sPESI, and age assessed whether hospitalization PEmb-QoL scores predicted three-month outcomes. The study protocol was approved by the Research Ethics Committee of the Mongolian National University of Medical Sciences (Approval No. 24/-25/10-1, June 12, 2025), and written informed consent was obtained from all participants prior to enrollment. Results: Mean age was 62.06 ± 17.5 years, and 46.4% of participants were male. Mean scores improved across all six domains at three months. Significant improvements were observed in symptom frequency, work-related problems, social limitations, symptom intensity, and emotional complaints (all p<0.05). Activities of daily living did not change significantly (p=0.332). Hospitalization PEmb-QoL scores significantly predicted three-month scores (p<0.001), independent of PESI, sPESI, and age. Conclusion Quality of life improved within three months after acute PE across most PEmb-QoL domains. Scores obtained during hospitalization predicted three-month outcomes. Early PEmb-QoL assessment may help identify patients at risk of persistent quality-of-life impairment and guide follow-up and rehabilitation.