In patients with acute pulmonary thromboembolism (PTE), the influence of residual pulmonary hypertension (PH) has not been well investigated. The aim of this study was to compare clinical characteristics between patients with and without residual PH, and to investigate the association between residual PH and clinical outcomes after acute phase in acute PTE. We included acute PTE patients who underwent echocardiogram after acute phase between January 2009 and December 2016. These patients were divided into residual PH and non-residual PH groups according to the value of estimated right ventricular systolic pressure (eRVSP) by echocardiogram after acute phase (the residual PH group: eRVSP ≥ 40 mmHg, the non-residual PH group: eRVSP < 40 mmHg). Kaplan–Meier survival curves were applied to investigate whether the residual PH were associated with PTE-related death or recurrent PTE in patients with acute PTE. A total of 49 patients with acute PTE were allocated into the residual PH group (n = 10) and non-residual PH group (n = 39). Median follow-up period for 49 patients was 7 months. The event-free survival rate was significantly lower in the residual PH group as compared with the non-residual PH group (p = 0.003), whereas there was no statistical significance between two groups stratified by initial PH or not (p = 0.97). Residual PH after acute phase was significantly associated with mid-term PTE-related death or recurrent PTE in patients with acute PTE.