Fanconi anaemia (FA) is an autosomal recessive inherited disease that renders patients susceptible to congenital anomalies, bone marrow failures, leukaemia, and solid malignancies. FA is caused by the loss of function of at least one gene in the FA/BRCA biological pathway, which is involved in DNA repair. Patients with FA have an increased risk of developing head and neck cancer, particularly oral squamous cell carcinoma (SCC). Due to susceptibility of head and neck cancer at a very young age, relatively poor survival rate, low tolerance to oncologic interventions, and complexity of treatments, strict follow-up is mandatory to detect any changes or recurrence of SCC in the head and neck region in FA patients. Surgery is the mainstay of treatment, but adjuvant therapy should be instituted when needed. This short report describes a rare case of lower lip SCC in FA and its management. It also highlights the impact of the COVID-19 pandemic on healthcare practices.