Pediatric surgery is a crucial pillar of health equity but is often not prioritized in the global health agenda, especially in low-and middle-income countries. Gastroschisis (GS) is a type of structural congenital anomaly that can be treated through surgical interventions. In Rwanda, neonatal surgical care is only available in one hospital. The experience of parents of children born with gastroschisis has not been previously studied in Rwanda. The objective of this study was to explore the lived experiences of parents of children diagnosed with GS in Rwanda. A qualitative study using a semi-structured interview guide was conducted. Parents who had children with gastroschisis and were discharged alive from the hospital in Rwanda were interviewed by trained data collectors, from May to July 2021. Data were transcribed, translated, and then coded using a structured code-book. Thematic analysis was conducted with the use of Dedoose software. Sixteen parents participated in the study. Five themes emerged from the data. They were: “GS diagnosis had a significant emotional impact on the parents”, “Parents were content with the life-saving medical care provided for their children despite some dissatisfaction due to the delayed initiation of care and shortage of medications”, “GS care was accompanied by financial challenges”, “support systems were important coping mechanisms” and “the impact of GS care extended into the post-discharge period”. Having a newborn with GS was an emotional journey. The lack of pre-knowledge about the condition created a shock to the parents. Parents found support from their faith and other parents with similar experiences. The experiences with the care received were mostly positive. The overall financial burden incurred from the medical treatment and indirect costs was high and extended beyond the hospital stay. Strengthening prenatal and hospital services, providing peer, spiritual and financial support could enhance the parents’ experience.