Purpose: The target disorders of emergency head CT are wide-ranging. Therefore, people working in an emergency department desire a computer-aided detection system for general disorders. In this study, we proposed an unsupervised anomaly detection method in emergency head CT using an autoencoder and evaluated the anomaly detection performance of our method in emergency head CT. Methods: We used a 3D convolutional autoencoder (3D-CAE), which contains 11 layers in the convolution block and 6 layers in the deconvolution block. In the training phase, we trained the 3D-CAE using 10,000 3D patches extracted from 50 normal cases. In the test phase, we calculated abnormalities of each voxel in 38 emergency head CT volumes (22 abnormal cases and 16 normal cases) for evaluation and evaluated the likelihood of lesion existence. Results: Our method achieved a sensitivity of 68% and a specificity of 88%, with an area under the curve of the receiver operating characteristic curve of 0.87. It shows that this method has a moderate accuracy to distinguish normal CT cases to abnormal ones. Conclusion: Our method has potentialities for anomaly detection in emergency head CT.