Objective Sex differences in short-term outcomes of patients with deep vein thrombosis (DVT) have been reported, but differences in long-term outcomes remain poorly characterized. This study aimed to evaluate sex differences in long-term mortality, venous thromboembolism (VTE)-related mortality, and bleeding-related mortality in patients with DVT at a tertiary care center. Methods A retrospective chart review from 2012 to 2018 of all consecutive patients diagnosed with DVT was performed. Patients were grouped by sex, and baseline characteristics and treatment modalities were compared. Long-term outcomes of recurrent VTE, bleeding, and related mortalities were analyzed. Multivariable regression analysis was performed to determine factors associated with overall mortality. Results A total of 1043 (female = 521 and male = 522) patients with DVT were captured in this study period. Female patients were older (64.7 vs 61.6 years old, p = 0.01) and less likely to be obese (68.2% vs. 71.1% , p = 0.04 ),but had a higher average Caprini score (6.73 vs 6.35, p = 0.04). There was no difference in anatomic extent of DVT, association with PE, and severity of PE between sexes. Most patients (80.5%) were treated with anticoagulation, with no differences in choice of anticoagulant or duration of anticoagulation between females and males. Male patients were more likely to undergo catheter-directed thrombolysis (CDT) for DVT (4.2% vs 1.7%, p = 0.02) and PE (2.7% vs 0.9%, p = 0.04). Female patients were more likely to receive systemic thrombolysis for PE (2.9% vs 1.1%, p = 0.05). After an average 2.3 years follow-up, there was significantly higher bleeding complications among females (22.2% vs 16.7%, p = 0.027). The overall mortality rate was 33.5% and not different between males and females. Females were more likely to experience VTE-related mortality compared to males (3.3% vs 0.6%, p = 0.002). On regression analysis, older age (OR = 1.04 [1.03–1.06]), cancer (OR = 7.64 [5.45–10.7]), and congestive heart failure (OR = 3.84 [2.15–6.86]) were independently associated with overall mortality. Conclusions In this study, there was no difference in overall long-term mortality between sexes for patients presenting with DVT. However, females had increased risk of long-term bleeding and VTE-related mortality compared to males.