In this study, the immunogenic and structural properties of ovalbumin (OVA) induced by pulsed electric fields (PEF) treatment were investigated. The immunogenic properties were estimated by the IgG and IgE binding abilities, which were determined by enzyme-linked immunosorbent assay (ELISA) using rabbit polyclonal antibodies and egg-allergy patients' sera, respectively. The structural changes were monitored by circular dichroism (CD), ultraviolet absorption, and fluorescence spectroscopy. When the OVA samples were treated at low electric field intensity (below 25 kV/cm, for 180 μs) or for short time (less than 60 μs, at 35 kV/cm), the IgG and IgE binding capacities gradually increased due to the partial unfolding of OVA. This was reflected in the increase in free SH content, surface hydrophobicity, and UV absorption. However, when the OVA samples were treated at high electric field intensity (exceeding 25 kV/cm, for 180 μs) or for long time (more than 60 μs, at 35 kV/cm), the IgG and IgE binding abilities significantly reduced due to the aggregation of OVA. This was also reflected in the decrease in free SH content, surface hydrophobicity, and UV absorption. Moreover, high-intensity PEF treatment caused a loss of the α-helix structure. The results showed that the largest decrease in the immunogenic properties was observed at 35 kV/cm for 180 μs. Therefore, PEF processing has the potential for utilization as a method for egg desensitization.