Systemic lupus erythematosus (SLE), induced by the interaction of susceptibility genes and environment risk factors, is a classical autoimmune diseases characterized by the dysregulation of innate and adaptive immune systems. Recently, evidence from genetic, cell biology and animal models suggested autophagy, a major pathway for organelle and protein turnover, plays a pivotal role in the occurrence and development of SLE, but not yet fully elucidated. We summarized an update on the recognized key principles of autophagy in SLE and focused our attention on the role of autophagy, including two main signaling pathways including mTOR and Beclin-1, in immune cells, such as B cell, T cell, neutrophils, etc. in SLE. Also, effects of currently used biological and chemical therapeutic drugs on autophagy in SLE were discussed. Autophagy may provide new targets for both diagnostic and therapeutic approaches for SLE although some results are still controversial, which worth more in-depth discussion in the future.