Background: There is an increasing prevalence of mental health problems among university student populations. In Indonesia, treatment rates are low among university students because of the high cost of treatment, stigma and the limited availability of mental care services. Internet-based interventions have been found to be effective in treating anxiety and depression in Western countries. However, little is known about the effectiveness of Internet-based interventions in low- and middle-income countries (LMICs) such as Indonesia. In this paper, we describe how we culturally adapted an Internet-based intervention to meet the needs of Indonesian students with depression and anxiety based on the theoretical framework of Barrera et al. (2013). Method: We culturally adapted a Western Internet-based student intervention for depression and anxiety. This intervention consists of 8 guided online sessions. 50 students from Universitas Gadjah Mada Yogyakarta who have mild to moderate depression or anxiety as assessed with the Patient Health Questionnaire-9 (PHQ-9) and Generalized Anxiety Disorder-7 (GAD-7), will participate in a feasibility study in which we will test participants’ satisfaction, system usability and uptake. Secondary outcomes include assessment of participants’ depression, anxiety and quality of life. Outcomes will be measured pre and post intervention. Discussion: The present paper presents the protocol of a pilot study aimed at assessing the feasibility and acceptability of a culturally adapted intervention for Indonesian university students with depression and anxiety. The results from the feasibility study will further guide the development of the intervention and may inform the protocol of a future randomized controlled trial (RCT) examining the effectiveness of the Internet-based intervention.