This study investigated the feasibility of administering motor assessments, delivering rehabilitation via parent-led activities, and enhancing motor function in children with complex congenital heart defects. Gross and fine motor development were evaluated in 20 toddlers ages 12 to 26 months after either a superior cavopulmonary connection (SCPC) procedure or an arterial switch operation (ASO) using the Peabody developmental scale, version 2 (PDMS-2). Feasibility of assessment and program delivery were examined using open-ended interviews with parents. The ASO group scored consistently higher than the SCPC group in every subscore of the PDMS-2 (ASO gross motor quotient, 96.78 ± 7.396 vs SCPC gross motor quotient, 77.56 ± 7.715 [P < 0.001]; ASO fine motor quotient, 101.20 ± 6.512 versus SCPC fine motor quotient, 87.70 ± 9.945 [P = 0.002]; ASO total motor quotient, 98.78 ± 6.515 versus SCPC total motor quotient, 79.56 ± 8.095 [P < 0.001]). A lower total motor quotient was associated with the use of anticoagulant medication (−20.3 ± 4.6; P < 0.001), longer and more frequent hospital stays (respectively, −3.6 ± 1 .4; P = 0.01 and −0.8 ± 0.4; P = 0.02), and shorter times between the most recent surgery and the assessment date (2.1 ± 0.5; P < 0.001). Age-standardized scores were constant between baseline and follow-up evaluation (baseline gross motor quotient, 87 ± 12 vs. post-intervention gross motor quotient, 88 ± 15 [P = 0.89]; baseline fine motor quotient, 94 ± 11 vs. post-intervention fine motor quotient, 94 ± 12 [P = 0.55]; baseline total motor quotient, 89 ± 12 vs. post-intervention total motor quotient, 90 ± 14 [P = 0.89]), indicating achievement of the expected rate of development. The most common barrier to home activity completion was illness in the SCPC group and lack of interest in the ASO group. Providing enjoyable activities and incorporating the activities into the participants’ schedules were keys to compliance. All the children were able to complete the assessments, and the parents reported a positive impact of the intervention on family life. Children who have had the SCPC procedure experience significant motor delays early in life. However, toddlers after ASO have age-appropriate motor skills. Completion of the rehabilitation program enables post-SCPC children to increase their rate of development to age-appropriate norms.