Complete fundoplication (Nissen) has long been accepted as the gold standard surgical procedure in children with therapy-resistant gastroesophageal reflux disease (GERD); however, increasingly more evidence has become available for partial fundoplication as an alternative. The aim of this study was to perform a systematic review and meta-analysis comparing complete versus partial fundoplication in children with therapy-resistant GERD. PubMed (1960 to 2011), EMBASE (from 1980 to 2011), and the Cochrane Library (issue 3, 2011) were systematically searched according to the PRISMA statement. Results were pooled in meta-analyses and expressed as risk ratios (RRs). In total, eight original trials comparing complete to partial fundoplication were identified. Seven of these studies had a retrospective study design. Short-term (RR 0.64; p = 0.28) and long-term (RR 0.85; p = 0.42) postoperative reflux control was similar for complete and partial fundoplication. Complete fundoplication required significantly more endoscopic dilatations for severe dysphagia (RR 7.26; p = 0.007) than partial fundoplication. This systematic review and meta-analysis showed that reflux control is similar after both complete and partial fundoplication, while partial fundoplication significantly reduces the number of dilatations to treat severe dysphagia. However, because of the lack of a well-designed study, we have to be cautious in making definitive conclusions. To decide which type of fundoplication is the best practice in pediatric GERD patients, more randomized controlled trials comparing complete to partial fundoplication in children with GERD are warranted.