The aim of this systematic review was to determine whether one-stage palatoplasty for children born with cleft lip and palate shows overall advantages in outcome compared with two-stage palatoplasty. The included studies were controlled studies of syndromic and non-syndromic children born with unilateral cleft lip and palate, bilateral cleft lip and palate, or isolated cleft palate. The interventions studied were one-stage palatoplasty and two-stage palatoplasty starting with the soft palate. The outcomes were facial growth, speech, hearing, presence of fistulae, other complications related to surgery, health-related quality of life, and health economics. In total, 14 original studies were included. Results were dichotomized into showing advantage for one- or two-stage palatoplasty for the respective outcome and compared with the results from six included systematic reviews. No overall advantage for either surgical strategy was found for any of the outcome measures. The certainty of evidence was highest for the presence of fistulae, followed by facial growth and speech. For several outcomes, the quality of the existing evidence was too low to allow for any conclusions to be drawn. Neither one- nor two-stage palatoplasty showed significant advantages in clinical outcomes compared with the other. Other aspects such as ethics, economics, or surgeon’s preference might hence be of more importance. Homogenous choices of outcome measures and defined minimal clinically important differences would facilitate further research.