Polygalacturonase (PG) is one of the most important enzymes related to the quality of vegetables, fruits and their products, it catalyzes the degradation of pectin. Cloudy juices may lose their turbidity by the action of pectin methylesterase and PG; hence it is important to have efficient methods to inactivate them. Pulsed light (PL) is a non-thermal method for food preservation based on the use of pulses of a high-intensity wide-spectrum light. Its ability to inactivate food enzymes has been demonstrated and has been related to absorption of UV light by proteins. The aim of this study was to investigate the capability of PL to inactivate PG, its kinetic and associated structural changes measured by chemical and fluorometric methods. PL was able to inactivate PG with a first-order kinetic constant of 0.0426 cm²/J; requiring 128 J/cm² to achieve 90 % inactivation. Disulfide bridges became broken during PL treatment as indicated by a 40 % increase in free sulfhydryl groups. Evidence of loss of tertiary structure was indicated by a decrease in intrinsic fluorescence intensity and changes in parameter A. The inactivation seems to proceed without transition states as observed in the phase-diagram analysis. In conclusion, PL is able to inactivate PG and the process is associated to rupture of disulfide bridges and changes in tertiary structure following a simple all-or-none process. Results show the capability of PL to inactivate PG, which may be useful to stabilize cloudy fruit juices.