The transition from traditional Teaching and Learning (T&L) methods (face-to-face) to Home-Based Learning (HBL) during the Covid-19 era is inevitable. Unfortunately, this transition not only creates positive effects but also has its own negative impact, especially for higher education students. Following on from that, this study was conducted to identify the challenges experienced by higher education students in Malaysia when following the HBL programme. In addition, this study also aims to determine the group of vulnerable students based on the location and type of residence. To achieve this goal, a survey was conducted on 2394 higher education students living throughout Malaysia. Inferential statistical analysis techniques (Principal Component Analysis & Kruskal Wallis) and descriptive (percentage & frequency) were used in this study to extract the raw data obtained. The results of the study show that higher education students in Malaysia usually face six main challenges when implementing HBL, namely decreased focus on learning (var(X)=20.26%), physical health problems (var(X)=12.12%), mental health problems (var(X)=10.06%), technical & connectivity problems (var(X)=10.82%), social isolation (var(X)=7.41%) and low digital literacy (var (X)=7.83%). The results of this study also found that students who live in rural and slum areas are the most vulnerable to the implementation of HBL. The findings of this study are very useful as supporting information for the authorities (stakeholders) to further strengthen the implementation of HBL in Malaysia.