We obtained ultraviolet photodissociation (UVPD) circular dichroism (CD) spectra of protonated L-phenylalanyl-L-alanine (L-H⁺PheAla) near the origin band of the S₀–S₁ transition using cryogenic ion spectroscopy. Infrared (IR) ion-dip, IR-UV hole burning (HB) and UV-UV HB spectra showed that L-H⁺PheAla existed as two different conformers in a cryogenic ion trap, and they had nearly identical peptide backbones but different conformations in the Phe side chain. The UVPD CD spectra revealed that the two conformers had opposite CD signs and significantly different CD magnitudes from each other. These results demonstrate that the CD value of L-H⁺PheAla near the origin band is strongly influenced by the conformation of the Phe side chain.