The upregulation of miR‐99a‐3p expression protected B cells from EIF4EBP1‐mediated autophagy, whilst the downregulation of miR‐99a‐3p expression induced autophagy via the EIF4EBP1‐mediated regulation of the autophagy signalling pathway in B cells isolated from individuals with SLE. Here, EIF4EBP1 is linked to systemic lupus erythematosus.