Background: Giardiasis is a common protozoal infection in cats, often treated with nitroimidazole derivatives such as metronidazole and secnidazole. However, there are concerns about resistance to nitroimidazoles and their adverse effects. Recent in vitro studies suggest that omeprazole, a proton pump inhibitor, exhibits anti-giardial effects by inhibiting giardial triosephosphate isomerase. No clinical studies have evaluated its efficacy in naturally infected cats. Objectives: This study aimed to assess and compare the anti-giardial efficacy of omeprazole, metronidazole, and secnidazole in cats naturally infected with Giardia duodenalis, based on faecal cyst shedding and clinical parameters. Methods: Forty-eight naturally infected cats were randomly assigned to four groups: omeprazole (1 mg/kg/day for 7 days), metronidazole (25 mg/kg twice daily for 7 days), secnidazole (30 mg/kg single dose), and placebo. Faecal cyst shedding was evaluated using the zinc sulphate flotation technique on days 0, 7 and 14. Faecal consistency was scored daily, and haematological parameters were assessed on days 0, 7 and 14. Results: By day 7, faecal cyst positivity was 50% in both the omeprazole and metronidazole groups, 58.3% in the secnidazole group, and 83.3% in the placebo group. The reduction observed in the omeprazole and metronidazole groups was statistically significant compared with the placebo (p < 0.05). By day 14, cyst positivity further decreased to 33.3% (omeprazole), 41.7% (metronidazole), and 50% (secnidazole), with omeprazole showing the lowest positivity rate among the treatments. Faecal scores improved significantly earlier in the omeprazole and metronidazole groups compared with secnidazole and placebo (p < 0.05). Conclusions: Omeprazole demonstrated promising anti-giardial efficacy, with reductions in cyst shedding and improvements in faecal consistency comparable to metronidazole. These findings suggest that omeprazole may serve as a potential alternative treatment option for feline giardiasis.