This prospective study sought to characterise the educational experiences, mental health, and behavioural functioning of Australian children with a pre-existing learning difficulty or specific learning disorder (SLD) during the COVID-19 pandemic. The study also evaluated the potential role of parent psychological distress as a risk factor for poorer child functioning in this high-risk population. Using a prospective longitudinal design, the study involved 58 parents of children and adolescents with a pre-existing learning difficulty or specific learning disorder (M age = 11.9 years; range 7–17 years) who were initially referred to a state-wide diagnostic centre for specific learning disorders in Melbourne, Victoria, Australia. Child outcomes were assessed using the COVID-19 Wellbeing and Mental Health Survey (a modified version of the CoRonavIruS Health Impact Survey [CRISIS] tool), the Strengths and Difficulties Questionnaire (SDQ), and the Emotional Distress Scale from the Patient-Reported Outcomes Measurement Information System (PROMIS). Parents’ mental health was assessed using the CRISIS tool and the Kessler Psychological Distress Scale (K10). In keeping with initial predictions, a large proportion of parents expressed significant disruption to child educational experience and routines, including challenges related to child engagement in remote learning platforms during COVID-19. Compared to pre-pandemic mental health symptom ratings, children experienced significantly higher symptoms of worry, negative thoughts, loneliness, agitation, and aggression during the pandemic period (all p < 0.05). As expected, higher levels of parent distress predicted greater child worry symptoms (p = 0.003) and more frequent child behavioural difficulties (p = 0.004). These results help elucidate the specific psychological and educational challenges faced by children with pre-existing learning difficulty or SLD during the COVID-19 pandemic. Family-centred intervention and/or supports may help to address the unique educational and psychological needs of young people with pre-existing learning differences and their families during future global pandemics.