Background: Pulmonary embolism (PE) is a common life-threatening disease, with mortality related to right ventricular (RV) dysfunction. Aims: To investigate the value of 3D global and regional right ventricular strain in patients with acute PE and at 1 month, as compared to a control population. Methods and Results: We conducted a longitudinal case-control prospective study, including 24 consecutive intermediate-risk PE patients. All patients underwent 2D and 3D transthoracic echocardiography within 12 hours of PE diagnosis and 1 month after hospital discharge. A control group was recruited, consisting of healthy volunteers matched on age and sex with PE patients. 3D RV echocardiographic sequences were analysed by commercial RV-specific software and output meshes were postprocessed to extract regional deformation. 3D echocardiographic 1-month follow-up was available in 18 patients. During acute PE, area strain was substantially altered in the RV free wall and within the trabecular septum. PE patients initially had RV dysfunction as assessed by 2D and 3D parameters. At follow-up, 2D parameters were restored compared to the control group, contrary to 3D RV area and circumferential strains. The McConnell’s sign was identified in 83% of patients and was associated with reduced apical and global RV area strain. Conclusions: Our 3D RV strain study demonstrates an incomplete recovery of 3D strain parameters 1 month after an episode of intermediate-risk acute PE despite restored 2D parameters. Further studies are required to assess the prognostic role and implications of this residual RV strain impairment after PE.