Background Haemodynamic alterations caused by acute pulmonary embolism (PE) may affect multi-organ function including kidneys. This multi-centre, multinational cohort study aimed to validate the prognostic significance of estimated glomerular filtration rate (eGFR) and its potential additive value to the current PE risk assessment algorithms. Methods The post hoc analysis of pooled prospective cohort studies: 2,845 consecutive patients (1,424 M/1,421 F, 66 ± 17 years) with confirmed acute PE and followed up for 180 days. We tested prognostic value of pre-specified eGFR level ≤60 mL/min/1.73 m2 calculated on admission according to the Modification of Diet in Renal Disease study equation. The primary outcome was all-cause 30-day mortality; the secondary outcomes were PE-related mortality, 180-day all-cause mortality, bleeding and composite outcome (PE-related death, thrombolysis or embolectomy). Results Two hundred and twenty-three patients (8%; 95% confidence interval [CI]: 7–9%) died within the first 30 days after the diagnosis. The eGFR on admission was significantly lower in non-survivors than in survivors (64 ± 34 vs. 75 ± 3 mL/min/1.73 m2, p < 0.0001). Independent predictors for a fatal outcome included: cancer, systolic blood pressure, older age, hypoxia, eGFR, heart rate and coronary artery disease. The eGFR of ≤60 mL/min/1.73 m2 independently predicted all-cause mortality (hazard ratio: 2.3; 95% CI: 1.7–3.0, p < 0.0001), PE-related outcome and clinically relevant bleedings (odds ratio: 0.90 per 10 mL/min/1.73 m2, 95% CI: 0.85–0.95, p = 0.0002). The eGFR assessment significantly improved prognostic models proposed by European guidelines with net re-classification improvement of 0.42 (p < 0.0001). Conclusion The eGFR of ≤60 mL/min/1.73 m2 not only independently predicted higher 30- and 180-day all-cause mortality and bleeding events, but when added to the current European Society of Cardiology risk stratification algorithm improved identification of both low- and high-risk patients. Therefore, eGFR calculation should be implemented in the risk assessment of acute PE.