BackgroundA longitudinal cohort study was established to investigate the well‐being of children born with cleft lip and/or palate (CL/P) during the COVID‐19 pandemic, in Victoria, Australia.Materials and MethodsThe Royal Children's Hospital cleft service database was used to identify children aged between 4 and 17 years old born with an isolated CL/P. Families of eligible children who consented to participate were asked to complete the Strengths and Difficulties Questionnaire (SDQ) between October and December 2020 and again 6‐month later. SDQ results from typically developing Australian children during the COVID‐19 pandemic were utilized from a previously published study.Results63 parents completed the baseline questionnaire, with 44 completing the 6‐month follow‐up. For participants at baseline, the mean age was 8.9 years, with 55% male. All outcome domains of the SDQ improved between baseline and timepoint 2, with the difference in total difficulties scores being statistically significant, indicating a reduction in total difficulties at timepoint 2, associated with the easing of COVID‐19 restrictions. When compared with the Australian population during the COVID‐19 pandemic, Victorian children born with CL/P had lower SDQ scores for all difficulties outcome domains, with statistically significant results for conduct problems, hyperactivity, peer problems and total difficulties, indicating fewer difficulties for children born with CL/P.ConclusionsChildren born with CL/P experienced fewer difficulties when compared with the typically developing Australian population during the COVID‐19 pandemic. The level of restrictions imposed because of the pandemic also had little influence on the well‐being of these children.