Cyclohexene skeletal isomerization, in a microcatalytic pulse reactor, was investigated using Al2O3 and AlPO4–Al2O3 as catalysts. Apparent rate constants and apparent activation energies were calculated according to the kinetic model of Bassett–Habgood. Selectivity studies concluded that 1-MCP and 3-MCP were competitive products with a first-order kinetics. The rate constants as well as the selectivity at 1-MCP increase with an increase in the number and strength of stronger acid sites, measured by means of the irreversible adsorption of aniline in cyclohexane, at 298 K, using a spectrophotometric method. The parallel reaction pathway, proposed for AlPO4 catalysts, agrees with both the observed rates and selectivities using Al2O3 and AlPO4–Al2O3 catalysts.