We aimed to compare the outcome of two different operative methods to correct pilonidal sinus disease (PSD) in children, i.e., excision and open wound care (OW) versus excision and primary transverse closure (PC) of the wound. In this retrospective, observational study, we extracted data from the medical records of 56 patients who underwent surgery for PSD at our institution between 1 January 2006 and 31 December 2016. To test whether the primary variable, i.e., rate of PSD recurrence, differed between the two surgical groups, a logistic regression model was fitted. Secondary explanatory variables were total length of stay (LOS) at the hospital, complications, sex and age of patients, seniority of the surgeon in charge, and volume of excised specimen. Overall, 32 (57%) children and young adults underwent OW, while 24 (43%) patients were treated by PC. Mean age at operation was 15.5 years in either group. PSD recurred in 12 of 32 (37.5%) children in the OW group and in 3 of 24 (12.5%) children in the PC group (ratio: 0.19, 95% confidence interval [95% CI] 0.03–1.07). Thus, treatment of primary PSD by PC proved superior with respect to PSD recurrence. Moreover, our study did not bring to light any high-grade complications in the PC group, and postoperative pain was minimal. Less invasive treatment approaches for chronic PSD are typically performed in an outpatient setting and offer reduced morbidity, low rates of PSD recurrence, and shortened periods of time to return to work or social activities. More radical operations of PSD should be reserved for recurrent PSD where less invasive approaches have failed several times.