The management of functional dyspepsia (FD) is a challenge for gastroenterologists in clinical practice. The eradication of Helicobacter pylori (H. pylori) and the utility of antacids, prokinetics and antidepressants are recommended as treatment choices for FD by consensus. Unlike in Europe and the USA, H. pylori eradication in Asia can lead to a higher proportion of FD patients with symptom relief and a higher symptom response rate to prokinetics. Moreover, response rates to anti-secretory drugs such as proton pump inhibitors deviate considerably from those in the Western world. Digestive enzymes and probiotics have also been reported to be used for the treatment of FD but evidence of their effectiveness is not adequate. Anti-anxiety drugs and antidepressants are reported to have peculiar effects on FD, especially in refractory FD, in which tricyclic antidepressants and selective serotonin reuptake inhibitors at small doses are most often recommended. When these drugs are selected to treat FD, clinicians should also consider their roles in treating mental disorders as well as the direct effects of neurotransmitters on gastroenterological disorders. However, their effects need to be further verified by prospective double-blinded randomized clinical trials with a large sample size. Distinguishing among different symptom subtypes has limited significance in guiding the medical choice for FD and individualized drug treatment should be recommended in its management.