Objective The impact of antithrombotic agents on primary intracerebral hemorrhage (ICH) patients remains controversial, especially with patients that require emergent craniotomy. This study was to evaluate clinical outcomes in operated ICH patients with and without prior antithrombotic agents. Methods This is a retrospective cohort study. Between January 2001 to December 2013, all ICH patients that received emergent craniotomy and is present in Taiwan's National Health Insurance Research Database were screened, and divided into prior antiplatelet therapy, anticoagulant therapy and non-antithrombotic therapy according to patient's healthcare claims data within 3 months of index admission. The primary endpoints included in-hospital mortality and complication, and short-term outcome. Results Of 18,872 eligible patients, 16,251 (87.1%) patients did not receive any antithrombotic therapy, 2,267 patients had antiplatelet therapy and 354 patients had anticoagulation therapy. After propensity score matching, significantly higher amount of blood transfusion and number of craniectomy was identified in the patients with prior antithrombotic treatment compared with non-antithrombotic therapy. In comparison with the non-antithrombotic treatment cohort, patients under prior anticoagulant treatment had significantly higher in-hospital mortality rate (Odds ratio, 2.12; 95% confidence interval, 1.45-3.10). Furthermore, during the 6-month follow-up period, prior anticoagulant therapy was independently associated with a greater risk of all-cause mortality rates (P = 0.001). Interestingly, the in-hospital and 6-month all-cause mortality of patients with prior antiplatelet treatment was not significantly different to patients with non-antithrombotic treatment. Conclusion These findings suggested an increased risk of in-hospital mortality and poor short-term outcome among operated ICH patients with prior antithrombotic therapy, particularly anticoagulant therapy, but not with antiplatelet therapy. .