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Background Type 2 diabetes mellitus (T2DM) and hypertension (HTN), both non-communicable diseases, are leading causes of death globally, with more imbalances in lower middle-income countries. Furthermore, poor treatment and management are known to lead to intensified healthcare utilization and increased medical care costs and impose a significant societal burden, in these countries, including Indonesia. Predicting future clinical outcomes can determine the line of treatment and value of healthcare costs, while ensuring effective patient care. In this paper, we present the prediction of length of stay (LoS) and mortality among hospitalized patients at a tertiary referral hospital in Tasikmalaya, Indonesia, between 2016 and 2019. We also aimed to determine how socio-demographic characteristics, and T2DM- or HTN-related comorbidities affect inpatient LoS and mortality. Methods We analyzed insurance claims data of 4376 patients with T2DM or HTN hospitalized in the referral hospital. We used four prediction models based on machine-learning algorithms for LoS prediction, in relation to disease severity, physician-in-charge, room type, co-morbidities, and types of procedures performed. We used five classifiers based on multilayer perceptron (MLP) to predict inpatient mortality and compared them according to training time, testing time, and Area under Receiver Operative Curve (AUROC). Classifier accuracy measures, which included positive predictive value (PPV), negative predictive value (NPV), F-Measure, and recall, were used as performance evaluation methods. Results A Random forest best predicted inpatient LoS (R2, 0.70; root mean square error [RMSE], 1.96; mean absolute error [MAE], 0.935), and the gradient boosting regression model also performed similarly (R2, 0.69; RMSE, 1.96; MAE, 0.935). For inpatient mortality, best results were observed using MLP with back propagation (AUROC 0.899; 69.33 and 98.61 for PPV and NPV, respectively). The other classifiers, stochastic gradient descent with regression loss function, Huber, and random forest models all showed an average performance. Conclusions Linear regression model best predicted LoS and mortality was best predicted using MLP. Patients with primary diseases such as T2DM or HTN may have comorbidities that can prolong inpatient LoS. Physicians play an important role in disseminating health related information. These predictions could assist in the development of health policies and strategies that reduce disease burden in resource-limited settings.