The mechanism of Brønsted acid‐initiated formal [1,3]‐rearrangement was rationalized using density functional theory (DFT) calculations. The computed mechanism comprises I) fragmentation: (a) imino‐nitrogen protonation, (b) proton transfer to olefin, (c) 1,2‐shift, and (d) C−C bond cleavage, and II) product formation: (e) methylene addition, (f) azonia‐[3,3]‐sigmatropic rearrangement, and (g) methylene elimination. The ene‐aldimine fragmentation to the 2‐azaallenium cation was found to be a highly reactive intermediate and the real catalyst species. The stereoselectivity for asymmetric formal [1,3]‐rearrangement of optically pure ene‐aldimine is in good agreement with chair transition state of azonia‐[3,3]‐sigmatropic rearrangement step and is supported by DFT calculation. Our computational study provides important mechanistic insights for ene‐aldimine rearrangements and guides the design of chiral catalysts for rearrangement process.