Background: Lifestyle risks for myopia are well known and the disease has become a major global public health issue worldwide. There is a relation between reading, writing, and computer work and the development of myopia. Methods: Within this prospective pilot study in 44 patients aged between 6 and 12 years with myopia we compared possible treatment effects of acupuncture or moxibustion. The diopters of the right and left eye were evaluated before and after the two treatment methods. Results: Myopia was improved in 14 eyes of 13 patients (15.9%) within both complementary methods. Using acupuncture an improvement was observed in seven eyes from six patients out of 22 patients and a similar result (improvement in seven eyes from seven patients out of 22 patients) was noticed in the moxibustion group. The extent of improvement was better in the acupuncture group (p = 0.008 s., comparison before and after treatment); however, group analysis between acupuncture and moxibustion revealed no significant difference. Conclusions: Possible therapeutic aspects with the help of evidence-based complementary methods like acupuncture or moxibustion have not yet been investigated adequately in myopic patients. Our study showed that both acupuncture and moxibustion can improve myopia of young patients. Acupuncture seems to be more effective than moxibustion in treating myopia, however group analysis did not prove this trend. Therefore, further Big data studies are necessary to confirm or refute the preliminary results.