To conduct a systematic review and meta-analysis of studies comparing the perimeatal-based flap (PBF) and tubularized incised-plate (TIP) techniques for primary hypospadias repair and determine whether the two techniques had similar reported outcomes. The PubMed, Embase and Cochrane databases were searched using the terms: hypospadias, Snodgrass, TIP*, tubularized incised plate, tubularized incised-plate, Mathieu*, perimeatal-based flap, perimeatal flap, meatal-based flap and meatal based flap. No other limits were used. Inclusion criteria included: primary hypospadias repair only; both including the PBF and TIP techniques; at least one of the quantitative outcomes obtainable from study; comparative studies. Twelve studies fulfilled the inclusion criteria and were included in the final analysis. Meta-analysis showed that there were no significant differences between the two techniques when comparing fistula (OR = 1.47; 95 % CI: 0.82-2.63; P = 0.20), meatal stenosis (OR = 0.53; 95 % CI: 0.24-1.16; P = 0.11), and wound dehiscence (OR = 0.82; 95 % CI: 0.24-2.84; P = 0.76). Both the studies which assessed cosmesis objectively showed a consistent better cosmetic result of the TIP technique (P < 0.05). There were no significant differences of complication rates between the two techniques, and the TIP technique was usually of better cosmesis. Given the large clinical heterogeneity among studies, future more well-designed studies with full data and uniform criterion were awaited.