Purpose—This study was conducted to develop an automated detection algorithm for screening fundus abnormalities, including age-related macular degeneration (AMD), diabetic retinopathy (DR), epiretinal membrane (ERM), retinal vascular occlusion (RVO), and suspected glaucoma among health screening program participants. Methods—The development dataset consisted of 43,221 retinal fundus photographs (from 25,564 participants, mean age 53.38 ± 10.97 years, female 39.0%) from a health screening program and patients of the Kangbuk Samsung Hospital Ophthalmology Department from 2006 to 2017. We evaluated our screening algorithm on independent validation datasets. Five separate one-versus-rest (OVR) classification algorithms based on deep convolutional neural networks (CNNs) were trained to detect AMD, ERM, DR, RVO, and suspected glaucoma. The ground truth for both development and validation datasets was graded at least two times by three ophthalmologists. The area under the receiver operating characteristic curve (AUC), sensitivity, and specificity were calculated for each disease, as well as their macro-averages. Results—For the internal validation dataset, the average sensitivity was 0.9098 (95% confidence interval (CI), 0.8660–0.9536), the average specificity was 0.9079 (95% CI, 0.8576–0.9582), and the overall accuracy was 0.9092 (95% CI, 0.8769–0.9415). For the external validation dataset consisting of 1698 images, the average of the AUCs was 0.9025 (95% CI, 0.8671–0.9379). Conclusions—Our algorithm had high sensitivity and specificity for detecting major fundus abnormalities. Our study will facilitate expansion of the applications of deep learning-based computer-aided diagnostic decision support tools in actual clinical settings. Further research is needed to improved generalization for this algorithm.