Background For patients diagnosed with acute pulmonary embolism (PE), the prognostic significance of concomitant right heart thrombi (RHT) lacks clarity. Methods We performed a meta-analysis of studies that enrolled patients with acute PE to assess the prognostic value of echocardiography-detectable RHT for the primary outcome of short-term all-cause mortality and the secondary outcome of short-term PE-related mortality. Unrestricted searches were conducted of PubMed and Embase from 1980 through January 31, 2016, and used the terms “right heart thrombi,” “pulmonary embolism,” and “prognos.*” A random effects model was used to pool study results; Begg rank correlation method was used to evaluate for publication bias; and I2 testing was used to assess for heterogeneity. Results Six of 79 potentially relevant studies met the inclusion criteria (15,220 patients). Overall, 99 of 593 patients with echocardiography-detectable RHT died (16.7% 95% CI, 13.8-19.9) compared with 639 of 14,627 without RHT (4.4% 95% CI, 4.0-4.7). RHT had a significant association with short-term all-cause mortality in all patients (OR, 3.0 95% CI, 2.2 to 4.1; I2  = 20%) and with PE-related death (three cohorts, 12,955 patients; OR: 4.8 95% CI, 2.0-11.3; I2  = 76%). Results were consistent for the prospective (two cohorts, 514 patients; OR, 4.8 95% CI, 1.7-13.6; I2  = 56%) and the retrospective (four cohorts, 14,706 patients; OR, 2.8 95% CI, 2.1 to 3.8; I2  = 0%) studies. Conclusions In patients diagnosed with acute PE, concomitant RHT were significantly associated with an increased risk of death within 30 days of PE diagnosis. Trial Registry PROSPERO registry; No.: CRD42016033960; URL: https://www.crd.york.ac.uk/prospero/