In this study, we analysed the statistical association between e-journal use and research output at the institution level in South Korea by performing comparative and diachronic analyses, as well as the analysis by field. The datasets were compiled from four different sources: national reports on research output indicators in science fields, two statistics databases on higher education institutions open to the public, and e-journal usage statistics generated by 47 major publishers. Due to the different data sources utilized, a considerable number of missing values appeared in our datasets and various mapping issues required corrections prior to the analysis. Two techniques for handling missing data were applied and the impact of each technique was discussed. In order to compile the institutional data by field, journals were first mapped, and then the statistics were summarized according to subject field. We observed that e-journal use exhibited stronger correlations with the number of publications and the times cited, in contrast to the number of undergraduates, graduates, faculty members and the amount of research funds, and this was the case regardless of the NA handling method or author type. The difference between the maximum correlation for the amount of external research funding with two average indicators and that of the correlation for e-journal use were not significant. Statistically, the accountability of e-journal use for the average times cited per article and the average JIF was quite similar with external research funds. It was found that the number of e-journal articles used had a strong positive correlation (Pearson’s correlation coefficients of r > 0.9, p < 0.05) with the number of articles published in SCI(E) journals and the times cited regardless of the author type, NA handling method or time period. We also observed that the top-five institutions in South Korea, with respect to the number of publications in SCI(E) journals, were generally across a balanced range of academic activities, while producing significant research output and using published material. Finally, we confirmed that the association of e-journal use with the two quantitative research indicators is strongly positive, even for the analyses by field, with the exception of the Arts and Humanities.