Cybersecurity has become one of the top priorities in Saudi Arabia, playing a key role in achieving Vision 2030 and advancing the kingdom’s position in digital transformation. This study investigates how cybersecurity knowledge, attitudes, and awareness influence user behaviours in health applications within Saudi Arabia. An online cross-sectional survey was distributed between March and April 2025 among Saudi Arabian residents. The collected data (n = 629) were analyzed using Smart PLS Structural Equation Modelling (SEM) to assess the relationships among the study constructs. The majority of the participants (61.4%) were between the age of 18 and 24, and 87.6% reported using health applications such as Sehhaty or Labayh to manage their health information. Results demonstrated that all three constructs significantly predicted cybersecurity behaviours: knowledge showed the strongest influence (β = 0.372), followed by attitude (β = 0.343) and awareness (β = 0.199), with all paths being statistically significant (p < 0.05). The model explained substantial variance in cybersecurity behaviours. Knowledge, attitude, and awareness significantly predict cybersecurity practices in healthcare application contexts. Findings highlight the critical need for targeted educational interventions focusing on cybersecurity knowledge enhancement and awareness programmes to promote safer digital health behaviours and strengthen patient data protection in Saudi Arabia’s healthcare system.