A new strategy for the synthesis of 3-aryl-4-methyl-5-O-substituted isoxazolines via tandem catalytic isomerization of O-allyl systems to O-(1-propenyl) systems—1,3-dipolar cycloaddition (1,3-DC) to nitrile oxides is presented. The influence of the heteroatom in Ph-X-CHCHCH3 (X=O, S, or Se) on the regio- and stereoselectivity of ArCNO 1,3-cycloaddition to these dipolarophiles is analyzed as well. The dipolarophiles were obtained via [RuClH(CO)(PPh3)3]–, [RuH2(CO)(PPh3)]– or base (KOH/18-crown-6)-catalyzed double bond migration in corresponding allyl ethers, O-allyl acetals, PhS– and PhSe–allyl systems. Cycloadditions of nitrile oxides to O-(1-propenyl) systems were fully regioselective whereas in the reactions of ArCNO with the PhS–(1-propenyl) and PhSe–(1-propenyl) systems both possible regioisomers were formed. It was established that within the majority of dipolarophiles of ROCHCHCH3 type 1,3-DC is concerted, while for some dipolarophiles of RXCHCHCH3 (X=O and R=Ph3C, 2,3-dihydroxypropyl, tetrahydropyran-2-yl; X=S or Se and R=Ph) type 1,3-DC turns into a two-step reaction with simultaneous rotation about C–C bond. The results of the experiments have been analyzed theoretically using DFT calculations. The results of these calculations agreed well with the experimental data.