Background Post-thrombotic syndrome (PTS) is a complication of deep vein thrombosis (DVT) and affects 20–40% of DVT subjects. The risk factor of PTS after DVT is difficult to determine. We aimed to evaluate the incidence of PTS after 3 months of DVT diagnosis and to determine the risk of PTS. Methods A retrospective cohort study of subjects who developed DVT confirmed by Doppler ultrasound in Cipto Mangunkusumo Hospital from April 2014 until June 2015. The presence of PTS was assessed after 3 months of completed DVT treatment using the Villalta score. Risk factors for PTS were evaluated from medical records. Results There were 91 subjects with DVT with mean age of 58 years. 56% were female. It was dominated by subjects aged ≥ 60 years (45.1%). Hypertension (30.8%) and diabetes mellitus (26.4%) were the major comorbidities in this study. Deep vein thrombosis occurred commonly in unilateral side (79.1%), proximal localization (87.9%), and unprovoked DVT (47.3%). The cumulative incidence of PTS after DVT was 53.8%, 69% of subjects had mild PTS. Heaviness of the leg (63.2%) and edema (77.5%) were the most common symptoms. Results There were 91 subjects with DVT with mean age of 58 years. 56% were female. It was dominated by subjects aged ≥ 60 years (45.1%). Hypertension (30.8%) and diabetes mellitus (26.4%) were the major comorbidities in this study. Deep vein thrombosis occurred commonly in unilateral side (79.1%), proximal localization (87.9%), and unprovoked DVT (47.3%). The cumulative incidence of PTS after DVT was 53.8%, 69% of subjects had mild PTS. Heaviness of the leg (63.2%) and edema (77.5%) were the most common symptoms. Significant risk factors for PTS were unprovoked DVT (adjusted RR 1.67; 95%CI: 1.17–2.04; p = 0.01) and female gender (adjusted RR 1.55; 95%CI: 1.03–1.94; p = 0.04). Age, body mass index, thrombus location, immobilization, malignancy and surgery was not associated with PTS. Conclusion We conclude that 53.8% of subjects suffered PTS after 3 months of DVT. Unprovoked DVT and female gender were significant risk factors for PTS.