The potential effects of asymptomatic flexible flatfoot (FF) on children’s health-related quality of life (QoL) and objective clinical foot characteristics have been poorly investigated in the literature. Therefore, this study aimed to analyse these indicators, comparing the children with asymptomatic FF and a control group. Methods: In total, 351 children were enrolled in this cross-sectional study—160 children with asymptomatic FF and 191 controls (children with normal feet). The children and their parents completed the Paediatric Quality of Life Inventory (PedsQLTM4.0). The objective foot characteristics included clinical foot posture measures, footprints, general hyperlaxity, and X-ray measurements. Results: Children with asymptomatic FF had a significantly lower QoL (overall and all four dimensions). The parents’ assessment of the QoL of their children with asymptomatic FF in most cases was lower compared to their children’s self-reported QoL. Moreover, almost all clinical foot measures also had significantly worse profiles among asymptomatic FF cases compared to the controls. This was observed with the Foot Posture Index-6 (FPI-6), the navicular drop (ND) test, the Chippaux–Smirak Index (CSI), Staheli’s Index (SI), the Beighton scale, and radiological angles (except the talo-first metatarsal angle). Conclusion: The findings suggest that asymptomatic FF not always reflects a normal foot development. This condition is related to decreased health-related quality of life, so the 5–10-year-old children’s and their parents’ complaints should be considered more closely in identification, treatment, and monitoring plans.