Propolis is a cereus resin with a complex chemical composition that possesses a wide range of biological activities. The aim of this study was to evaluate the in vitro anti-Giardia lamblia activity of Sonoran propolis collected from three different areas of Sonoran Desert in northwestern Mexico (Caborca, Pueblo de Alamos, and Ures) and some of its chemical constituents. Additionally, we also analyzed the seasonal effect on the anti-G. lamblia activity of propolis. G. lamblia trophozoite cultures were treated with different concentrations of Sonoran propolis or chemical compounds during 48 h cell proliferation and cell viability were determined. Ures propolis showed the highest inhibitory activity against G. lamblia (IC50 63.8 ± 7.1 µg/mL) in a dose-dependent manner (Ures > Pueblo de Alamos > Caborca). Season had a significant effect on the in vitro anti-G. lamblia activity of Ures propolis. Summer propolis showed the highest inhibitory effect on the G. lamblia trophozoite growth (IC50 23.8 ± 2.3 µg/mL), followed by propolis collected during winter (IC50 59.2 ± 34.7 µg/mL), spring (IC50 102.5 ± 15.3 µg/mL), and autumn (IC50 125.0 ± 3.1 µg/mL). Caffeic acid phenethyl ester, an Ures propolis exclusive constituent, had the highest growth-inhibitory activity towards G. lamblia [IC50 63.1 ± 0.9 µg/mL (222.1 ± 3.2 µM)]. To our knowledge, this is the first study showing that caffeic acid phenethyl ester possesses antiparasitic activity against G. lamblia. Naringenin [IC50 125.7 ± 20.7 µg/mL (461.8 ± 76.3 µM)], hesperetin [IC50 149.6 ± 24.8 µg/mL (494.9 ± 82.2 µM)], and pinocembrin [IC50 174.4 ± 26.0 µg/mL (680.6 ± 101.7 µM)] showed weak anti-G. lamblia activity. On the other hand, chrysin and rutin did not show significant antiparasitic activity. In conclusion, our results suggest that Sonoran propolis and some of its chemical constituents had inhibitory effects on the in vitro growth of G. lamblia trophozoites.