Cognitive functioning across development has predominantly been assessed through task performance. However, the role of cognitive effort infants and young children exert has been largely neglected in understanding cognitive functioning. In a large longitudinal sample (YOUth cohort, N = 2241) of infants and young children aged 5, 10 and 36 months, we extracted dynamic baseline-corrected pupil responses to measure cognitive effort during a gap-overlap eye-tracking task. Results revealed a shift from predominantly reactive effort when infants were younger to more preparatory effort in older children, especially for the more demanding condition. Moreover, preparatory effort in infancy predicted cognitive effort in childhood. These findings underscore the importance of measuring cognitive effort in addition to task performance to capture a more complete picture of early cognitive development.