Three novel amphiphilic alloxazinium salts were prepared: 3-dodecyl-5-ethyl-7,8,10-trimethylisoalloxazinium perchlorate (1c), 1-dodecyl-5-ethyl-3-methylalloxazinium perchlorate (2b), and 3-dodecyl-5-ethyl-1-methylalloxazinium perchlorate (2c). Their catalytic activity in thioanisole (3) oxidation with hydrogen peroxide was investigated in micelles of sodium dodecylsulfate (SDS), hexadecyltrimethylammonium nitrate (CTANO3) and Brij 35. Reaction rates were strongly dependent on the catalyst structure, on the type of micelles, and on pH value. Alloxazinium salts 2 were more effective catalysts than isoalloxazinium salts 1. Due to the contribution of micellar catalysis, the vcat/v0 ratio of the catalyzed and non-catalyzed reaction rates was almost 80 with salt 2b solubilized in CTANO3 micelles. Nevertheless, the highest acceleration was observed with non-amphiphilic 5-ethyl-1,3-dimethylalloxazinium perchlorate (2a) in CTANO3 micelles (vcat/v0 = 134). In this case, salt 2a presumably acts as a phase-transfer catalyst bringing hydrogen peroxide from the aqueous phase into the micelle interior. Synthetic applicability of the investigated catalytic systems was verified on semi-preparative scale.