The aim of the study was to evaluate the therapeutic value and possible mechanisms of transcutaneous electroacupuncture (TEA) in a double-blind and cross-over study in patients with functional dyspepsia (FD). Twenty-seven patients with FD were enrolled and the study consisted of two parts: (i) acute effects of TEA at PC6 and ST36 on gastric slow waves and heart rate variability and (ii) chronic (2 weeks) effects of TEA at PC6 and ST36 on dyspepsia symptoms, gastric slow waves, heart rate variability and neuropeptide Y (NPY) and motilin. The results of this study are: (i) The dyspepsia symptom score was decreased by 55% at the end of chronic TEA and the improvement was significant (P < 0.01); (ii) the high frequency (HF) assessed from the spectral analysis of heart rate variability was markedly increased with both acute TEA (76% increase, P = 0.01) and chronic TEA (75% increase, P = 0.025); (iii) gastric slow waves were not altered by either acute or chronic TEA; and (iv) the plasma level of NPY but not motilin was increased after chronic TEA. Non-invasive and needleless transcutaenous electroacupuncture at ST36 and PC6 markedly improves dyspepsia symptoms and the improvement may be associated with the increase in HF heart rate variability and the modulation of NPY.