Background. Electroacupuncture (EA) has been reported to treat functional constipation (FC). The aim of this study was to investigate the efficacy and safety of EA with different needle insertion method for FC. Methods. Sixty-seven participants were randomly assigned to control (EA with shallow puncture) and EA (with deep puncture) groups. Every patient received 5 treatments per week in the first two weeks, then 3 treatments per week during the following six weeks. Complete spontaneous bowel movements (CSBM), spontaneous bowel movements (SBM), Bristol stool scores (BSS), and Patient Assessment of Constipation Quality of Life (PAC-QOL) were assessed. Results. Both shallow and deep EA significantly increased CSBM frequency compared to the baseline. CSBM was increased from 0.50 ± 0.59/wk to 2.00 ± 1.67/wk with deep EA and from 0.48 ± 0.59/wk to 1.33 ± 1.09/wk with shallow EA (P < 0.05, resp.). Similar finding was noted in SBM. Deep EA was more potent than shallow EA (P < 0.05) during the treatment period. No difference was found on BSS and PAC-QOL between two groups. Conclusion. It is effective and safe with EA to treat FC. Studies with large sample size and long-term observation are needed for further investigation.