The coronavirus disease 2019 (COVID-19) pandemic is an unprecedented public health crisis worldwide. This pandemic has led to the spread of online misinformation, closure of schools, postponement of re-opening of schools, and restrictions on healthy outdoor activities. These, in turn, have caused a disruption in the daily life of middle school students. This study aimed to identify the relationships between eHealth literacy, awareness of pandemic infectious diseases, and healthy lifestyle in middle school students. For this purpose, we conducted a descriptive, correlational study in two cities in the capital of South Korea. A total of 138 middle school students completed self-reported questionnaires about eHealth literacy, awareness of pandemic infectious diseases, and healthy lifestyle. Middle school students displayed moderate levels of eHealth literacy (3.72 ± 0.97), awareness of pandemic infectious diseases (3.33 ± 0.92), and healthy lifestyle (2.98 ± 0.72). Positive correlations were found between eHealth literacy and awareness of pandemic infectious diseases (r = 0.44, p < 0.001), between eHealth literacy and healthy lifestyle (r = 0.52, p < 0.001), and between awareness of pandemic infectious diseases and healthy lifestyle (r = 0.38, p < 0.001). These findings suggest that eHealth literacy may be an important aspect of increasing the awareness about pandemic infectious diseases and forming healthy lifestyle habits in Korean middle school students during the COVID-19 pandemic.