Chronic abdominal pain has many etiologies, one of them being parasites. The aim of this study was to find an association between chronic abdominal pain in children and Blastocystis hominis (Bh). Clinical files of patients with Bh and functional abdominal pain were reviewed. A comparison was made between patients who showed an improvement of their symptoms and those who did not. Out of the 138 patients who had functional abdominal pain and Bh, 37 patients did not receive any treatment (26.8%), while 101 received it and were treated with different antimicrobial agents (73.2%); regarding the improvement of symptoms, a statistically significant difference (p < 0.001) was observed. Chronic abdominal pain in children has different etiologies; however, we have documented through this work that it is appropriate to provide antimicrobial treatment for patients with Bh and chronic abdominal pain.