Introduction Pharmacy students should be eHealth literate by being skilful in searching, evaluating and applying online health information. Mobile health applications should be utilised when making clinical decisions to achieve optimal patient care with the ever-changing pharmacy practice. This study aims to explore the eHealth literacy and mobile health application utilisation amongst pharmacy undergraduates. Methods A cross-sectional study was conducted from March to April 2021. An online survey, consisting of socio-demographic characteristics, Internet use, eHealth Literacy Scale and mobile health application utilisation, was distributed amongst pharmacy undergraduates in public and private universities in Malaysia. Data analysis included descriptive statistics, one-way analysis of variance test, Mann–Whitney U test and Kruskal–Wallis test Results A total of 415 participants completed the survey (response rate = 82.5%). The median eHealth Literacy Scale score (out of 40) was 31.0 ± 3.0 (interquartile range). More than one-third of participants (34.7%) were found to have low eHealth literacy. Many lacked confidence in making health decisions from online information (42.4%) and skills in distinguishing between high-quality and low-quality health resources (35.2%). Only 70.4% of the participants had mobile health applications installed on their smartphones and/or tablets. Some students felt that they were neither knowledgeable nor skilful enough to utilise mobile health applications (24.8%), whereas 23.9% were unaware of the mobile health applications available. Conclusion In summary, the eHealth literacy of Malaysian pharmacy students can be further enhanced by incorporating eHealth literacy-focused programmes into the curriculum. Moreover, pharmacy students’ mobile health application utilisation can be improved through increased awareness and support from universities.