In Korea, patients with mild cognitive impairment can choose to receive treatment of Korean medicine, and Korean medicine hospitals provide specialized medical care for the prevention and management of cognitive disorders. The aim of the study is to explore the role of Korean medicine therapy for patients with mild cognitive impairment in a real clinical setting. Fifteen patients with amnestic mild cognitive impairment were enrolled in this prospective observational study in three Korean medicine hospitals. Korean medicine treatments were delivered by experienced professionals and not restricted to standardized treatment. Outcome measures were prospectively planned to examine the Korean-Montreal Cognitive Assessment (K-MoCA), Korean-Mini Mental State Examination (K-MMSE), and other detailed neuropsychological assessment at the baseline and after 12 and 24 weeks of treatment. Korean medicine treatment for MCI treatment in the real-world clinical setting included herbal medicine and acupuncture. The most frequently used herbs in herbal decoctions were Acori Graminei Rhizoma, Polygalae Radix, and Poria Sclerotium Cum Pini Radix. The herbal medicine formulae used in this study were classified into three categories: tonifying Qi (33.3%), tonifying kidney (46.7%), and calming liver (20%) formulae. In the cognitive ability assessment, the K-MoCA score significantly improved after treatment (mean difference 2.6; 95% CI: 1.3 to 3.9, p=0.001). The K-MMSE score slightly increased after treatment; however, the improvement was not statistically significant (mean difference 0.8; 95% CI: −0.5 to 2.0, p=0.195). In detailed neuropsychological assessment, the cognitive domains of executive functions and memory after the treatment were distinctively improved. In this prospective observational case series, we could see the real clinical environments of treating patients with mild cognitive impairment in Korean medicine hospitals. Patients treated with Korean medicine showed improved results in the neuropsychological assessment after 12 and 24 weeks.