Background: Depressive disorders (DD) affect not only mood and behavior but also various physical functions. Traditional Chinese medicine (TCM) has been shown to have some benefits in treating DD. However, one formula or one single herb might be not show high efficacy when used to treat depression. Thus, this study aimed to examine the core prescription pattern of Chinese herbal medicine (CHM) among patients with DD in Taiwan as a reference for related research and clinical applications. Methods: All patients, who had been diagnosed with major depressive disorder or minor depression or dysthymia without any other baseline diseases and had at least one CHM outpatient clinical visit from 2002 to 2011, were extracted from three randomly sampled cohorts, namely the 2000, 2005 and 2010 cohorts of the National Health Insurance Research Database (NHIRD) of Taiwan. The collected data was analyzed to explore the patterns of herbal products. Results: There were 197,146 patients with a diagnosis of DD and of these 1806 subjects had only a diagnosis of DD and utilized CHM. The most common formula was Gan-Mai-Da-Zao-Tang (12.19%), while Suan-Zao-Ren (3.99%) was the most commonly prescribed single herb. The core pattern of prescriptions consisted of a combination of Gan-Mai-Da-Zao-Tang, Jia-Wei-Xiao-Yao-San, Chai-Hu-Jia-Long-Gu-Mu-Li-Tang, He-Huan-Pi, Yuan-Zhi and Shi-Chang-Pu. Conclusions: This study describes the CHM core prescription pattern used to treat patients in Taiwan with DD and it is a potential candidate for study in future pharmacological or clinical trials targeting DD.