Background/Objectives: Acute pulmonary embolism (PE) is a major cause of cardio-vascular mortality, with prognosis influenced by hemodynamic status, comorbidities, and biomarker profiles. Although several laboratory markers have demonstrated prog-nostic relevance in PE, it remains unclear whether their predictive performance differs in patients with active malignancy. This study aimed to identify laboratory predictors of in-hospital mortality in acute PE and to evaluate the modifying effect of malignancy on biomarker-based prognostic stratification. Methods: This retrospective multicenter cohort study included 2803 consecutive patients with computed tomography-confirmed acute PE enrolled in the Regional Pulmonary Embolism Registry (REPER) between January 2015 and April 2026. Univariate and multivariable logistic regression analyses were performed to identify predictors of in-hospital mortality in the overall cohort and in subgroups stratified by malignancy status. Interaction analyses were used to assess effect modification by malignancy. Results: Active malignancy was present in 14.02% of patients, while overall in-hospital mortality was 14.93%. In the overall cohort, multivariable analysis identified malignancy (OR 1.698, 95% CI 1.128–2.555, p = 0.011), C-reactive protein (CRP), glucose, creatinine clearance (CrCl), platelet count, and white blood cell count as independent predictors of in-hospital mortality (BNP was excluded from multivariable models due to missing data). Mortality was significantly higher in patients with ma-lignancy compared with those without (20.9% vs. 13.2%, p < 0.001). In patients with malignancy, CRP and glucose remained independent predictors, whereas in non-malignant patients, CRP, glucose, and CrCl were independently associated with mortality. Significant interaction effects were observed for CrCl, age, glucose, and white blood cell count. Conclusions: Malignancy is an important predictor of in-hospital mortality in acute PE and may partially influence the prognostic performance of certain conventional biomarkers. These findings suggest that while standard risk markers remain broadly reliable, specific parameters might benefit from a cautious, malignancy-aware interpretation.