2-Hydroxy-3-ethylidene-5-(methoxycarbonyl)-3,4-dihydro-2H-pyran-4-acetic acid 2-(3,4-dihydroxyphenyl)ethyl ester (3,4-DHPEA-EA) is a kind of secoiridoid first found in three Japanese olive pomaces: Mission, Lucca, and Manzanillo. These varieties showed high activity of 3,4-DHPEA-EA as an antiallergic active substance with IC50 at 33.5 ± 0.6 μg/mL. Because 3,4-DHPEA-EA was the most abundant among the active substances in the pomaces and the activity of 3,4-DHPEA-EA was greater than that of hydroxytyrosol and elenolic acid, 3,4-DHPEA-EA, which has the ester linkage of hydroxytyrosol and elenolic acid, should be essential for antiallergic activity. Although a trace amount (1.04 mg/kg) of luteolin in the pomace showed the highest antiallergic activity with IC50 at 0.752 ± 0.1 μg/mL, we concluded that the entire antiallergic effect derives from the abundance of 3,4-DHPEA-EA, especially in the green olive pomace of the Mission variety in October, which showed the highest level of 3,4-DHPEA-EA (5033 ± 118 mg/kg). Therefore, the Mission variety had the most effective antiallergy property.