For appropriate treatment, accurate discrimination between seborrheic dermatitis and psoriasis in a timely manner is crucial to avoid complications. However, when they occur on the scalp, differential diagnosis can be challenging using conventional dermascopes. Thus, we employed smartphone-based multispectral imaging and analysis to discriminate between them with high accuracy. A smartphone-based multispectral imaging system, suited for scalp disease diagnosis, was redesigned. We compared the outcomes obtained using machine learning-based and conventional spectral classification methods to achieve better discrimination. The results demonstrated that smartphone-based multispectral imaging and analysis has great potential for discriminating between these diseases.