Background: To compare ocular and corneal inherent aberrations in the naked eyes of randomly selected children fitted with MiSight contact lenses (CL) for myopia control, versus children corrected with single-vision spectacles (control), over a 24-months period. Methods: Children aged 8 to 12 years, with myopia (-0.75 to -4.00 D sphere) and astigmatism (< -1.00 D cylinder), were assigned to the lens study group (MiSight) or the control group (single-vision spectacles). Axial length (AL) was measured by biometry, the root mean square aberration (RMS) was determined as corneal (RMS_C), corneal high order RMS (HO_RMS_C), corneal low order RMS (LO_RMS_C), ocular total RMS (RMS_T), ocular total high order RMS (HO_RMS_T), ocular total low order RMS (LO_RMS_T), corneal spherical aberration (SA_C) and ocular total SA (SA_T) were calculated by aberrometric measures at the baseline, and on 12- and 24-months visits. A 5 mm diameter was defined for the analysis in all visits for all subjects. Only the dominant eye was analyzed. Results: Seventy-four subjects completed the clinical trial: 41 subjects from the MiSight group (age: 11.01 ± 1.23 years) and 33 from the single-vision group (age: 10.12 ± 1.38 years). In the control group, RMS_T (0.57 ± 0.20 µm, p = 0.029) and LO_RMS_T (0.46 ± 0.18 µm, p = 0.047) registered significant changes after 24-months in the control group. In the MiSight group no significant changes were registered. The SA_C and SA_T did not reveal significant changes between visits or between groups. Conclusions: The wear of MiSight CL did not induce significant changes in aberrations in anterior cornea and contrary of control group the total ocular RMS and low order RMS did not significantly caused by significantly lower eye growth and myopia progression. The naked eye results obtained in present study allow to predict that children do not develop basal corneal or total aberration changes in response of wearing MiSight lens along the time.Trial registration: ClinicalTrials.gov Identifier: NCT01917110.