Since a high dropout rate for university students is a significant risk to local communities and countries, a dropout prediction model using machine learning is an active research domain to prevent students from dropping out. However, it is challenging to fulfill the needs of consulting institutes and the office of academic affairs. To the consulting institute, the accuracy in the prediction is of the utmost importance; to the offices of academic affairs and other offices, the reason for dropping out is essential. This paper proposes a Student Dropout Prediction (SDP) system, a hybrid model to predict the students who are about to drop out of the university. The model tries to increase the dropout precision and the dropout recall rate in predicting the dropouts. We then analyzed the reason for dropping out by compressing the feature set with PCA and applying K-means clustering to the compressed feature set. The SDP system showed a precision value of 0.963, which is 0.093 higher than the highest-precision model of the existing works. The dropout recall and F1 scores, 0.766 and 0.808, respectively, were also better than those of gradient boosting by 0.117 and 0.011, making them the highest among the existing works; Then, we classified the reasons for dropping out into four categories: “Employed”, “Did Not Register”, “Personal Issue”, and “Admitted to Other University.” The dropout precision of “Admitted to Other University” was the highest, at 0.672. In post-verification, the SDP system increased counseling efficiency by accurately predicting dropouts with high dropout precision in the “High-Risk” group while including more dropouts in total dropouts. In addition, by predicting the reasons for dropouts and presenting guidelines to each department, the students could receive personalized counseling.