Aim. Laparoscopic Nissen fundoplication (LNF) and Stretta radiofrequency (RF) are used as main alternative strategies to manage medication-refractory GERD. This study was therefore prospectively evaluated outcomes of patients with refractory GERD 5 years after LNF or Stretta RF. Methods. A total of 215 consecutive patients with refractory GERD underwent LNF (N.=102) and Stretta RF (N.=113) in our department between 2007 and 2008. They were followed-up for 5 years, during which the outcome measures including symptom scores of regurgitation, heartburn, chest pain, belching, hiccup, cough and asthma as well as the proton pump inhibitor (PPI) use and complications. Results. Of the 215 patients, 179 patients following LNF (N.=87) or Stretta RF (N.=92) completed the designated 5-year follow-up and were included in the final analysis. At the end of 5-year follow-up, the post-treatment scores were statistically lower as compared with the pre-treatment scores in both groups, while the symptom improvements after Stretta were significantly lower than that after LNF (p < 0.05). Besides, 81 (91%) patients achieved complete PPI therapy independence after LNF, comparing with 47 (51.1%) after Stretta RF (P<0.05). No significant differences in post-treatment complications were observed except for the abdominal distention. Conclusion. Even though laparoscopic Nissen fundoplication and Stretta RF are capable of controlling GERD symptoms effectively and safely in selected patients, LNF could improve more in symptoms and PPI elimination.