Background: The purpose of this study was to investigate the incidence and timing of postoperative symptomatic pulmonary embolism (PE) in patients receiving non-warfarin following primary total joint arthroplasty (TJA), to clarify the appropriate duration of postoperative VTE prophylaxis. Methods: We retrospectively reviewed the medical records of 11148 patients who underwent primary TJA, including total knee arthroplasty (TKA) and total hip arthroplasty (THA) at our institution from January 2012 to March 2019. The median postoperative day of diagnosis of symptomatic PE and interquartile range for day of diagnosis were determined. Multivariate Cox proportional hazards modeling was used to test the difference of timing for PE based on demographics and comorbidities. Results: The overall 90-day rate of symptomatic PE was 0.71%. The median day of diagnosis for symptomatic PE was 3 day postoperatively (interquartile: 2–7 day). Factors that showed statistical significance on multivariate analysis in association with earlier timing of PE occurrence in patients with atrial fibrillation, diabetes mellitus, coronary heart disease and history of stroke. Conclusion: The vast majority symptomatic PE occurs in the early postoperative period after TJA, and atrial fibrillation, diabetes mellitus, coronary heart disease and history of stroke were independent factors affecting the timing of symptomatic PE.