Background In any health care system, both the classification of data and the confidence level of such classifications are important. Therefore, a selective prediction model is required to classify time series health data according to confidence levels of prediction. Objective This study aims to develop a method using long short-term memory (LSTM) models with a reject option for time series health data classification. Methods An existing selective prediction method was adopted to implement an option for rejecting a classification output in LSTM models. However, a conventional selection function approach to LSTM does not achieve acceptable performance during learning stages. To tackle this problem, we proposed a unit-wise batch standardization that attempts to normalize each hidden unit in LSTM to apply the structural characteristics of LSTM models that concern the selection function. Results The ability of our method to approximate the target confidence level was compared by coverage violations for 2 time series of health data sets consisting of human activity and arrhythmia. For both data sets, our approach yielded lower average coverage violations (0.98% and 1.79% for each data set) than those of the conventional approach. In addition, the classification performance when using the reject option was compared with that of other normalization methods. Our method demonstrated superior performance for selective risk (12.63% and 17.82% for each data set), false-positive rates (2.09% and 5.8% for each data set), and false-negative rates (10.58% and 17.24% for each data set). Conclusions Our normalization approach can help make selective predictions for time series health data. We expect this technique to enhance the confidence of users in classification systems and improve collaborative efforts between humans and artificial intelligence in the medical field through the use of classification that considers confidence.