(R)‐β‐piperonyl‐γ‐butyrolactones are key building blocks for the synthesis of podophyllotoxin, which have demonstrated remarkable potential in cancer treatment. Baeyer–Villiger monooxygenases (BVMOs)‐mediated asymmetric oxidation is a green approach to produce chiral lactones. While several BVMOs were able to oxidize the corresponding cyclobutanone, most BVMOs gave the (S) enantiomer while Cyclohexanone monooxygenase (CHMO) from Brevibacterium sp. HCU1 gave (R) enantiomer, but with a low enantioselectivity (75% ee). In this study, we use a strategy called “focused rational iterative site‐specific mutagenesis” (FRISM) at residues ranging of 6 Å from substrate. The mutations by using a restricted set of rationally chosen amino acids allows the formation of a small mutant library. By generating and screening less than 60 variants, we achieved high ee of 96.8%. Coupled with the cofactor regeneration system, 9.3 mM substrate was converted completely in a 100‐mL scale reaction. Therefore, our work reveals a promising synthetic method for (R)‐β‐piperonyl‐γ‐butyrolactone with the highest enantioselectivity, and provides a new opportunity for the chem‐enzymatic synthesis of podophyllotoxin.