Students have been confined to their homes to attend online classes during Covid-19 pandemic. This study aimed to estimate the effect of the Covid-19 Home Confinement on the prevalence and associated risk factors of low back pain, among university students in Malaysia. A total of 366 university students (155 males and 211 females) aged between 18 and 25 years participated in this cross-sectional study. A self-administered structured questionnaire on socio-demographic factors and associated risk factors was used. The prevalence of low back pain among university students before Movement Control Order (MCO) was 22.7%, while after MCO, the prevalence was 37.2%. The prevalence of LBP in females was 45.0% and males was 26.5%. Stepwise regression analysis showed that prolonged sitting, prolonged standing, being female, third year student and being obese significantly contributed to the occurrence of low back pain among university students during Covid-19 home confinement. The Covid-19 Home Confinement resulted in a significant increase in the prevalence of low back pain.