Background: The objective was to evaluate the prevalence of latent trigger points (LTrPs) in lower limb muscles in participants with a high medial longitudinal arch (MLA) of the foot compared to controls. Methods: Participants with a navicular drop test of 4–9 mm were included in the control group; the high MLA group included navicular drop test values of ≤4 mm. The presence of LTrPs was assessed by palpation techniques. The muscles evaluated were medial gastrocnemius (LTrP1), lateral gastrocnemius (LTrP2), soleus (LTrP1), peroneus longus, peroneus brevis, tibialis anterior, extensor digitorum longus, flexor digitorum longus, rectus femoris, vastus medialis (LTrP1 and LTrP2), and the vastus lateralis of the quadriceps (LTrP1 and LTrP2). Results: Thirty-seven participants with high MLA and thirty-seven controls were included in the study. Twenty-nine (78.4%) participants in the high MLA group had at least 1 LTrP, compared to twenty-three (62.2%) in the control group. No statistical difference (p < 0.05) was found in the total number of LTrPs between groups (4.46 ± 3.78 vs. 3.24 ± 3.85). There were more participants (p < 0.05) with LTrPs in the tibialis anterior, extensor digitorum longus, and vastus lateralis (LTrP1 and LTrP2) in the high MLA group than in the control group. Conclusion: Although no differences were found in the number of total LTrPs between groups, the prevalence was statistically significantly higher in the tibialis anterior, extensor digitorum longus, and vastus lateralis of the participants with high MLA of the foot.