Well-being in children with a complex medical condition (CMC) impacts the way they view and communicate with their immediate environment as well as their development, and it is thus necessary to inquire about the contextual issues and different needs that a CMC carries. This pilot study aimed to identify factors of pediatric well-being from the experience of hospitalization and convalescence of youth with CMC and their caregivers, in a cross-sectional analysis using a selective methodology complemented by an indirect observational methodology. We analyzed the quality of life and well-being of youth with CMC using a validated KINDLR questionnaire. We collected 35 surveys: 11 from youth with CMC and 24 from caregivers from Spain. We focused the analysis on sociodemographics, well-being perceptions, and coping strategies variables. The results show that children aged between 3 and 6 years and their caregivers scored physical well-being the lowest out of all dimensions of well-being, and they scored family well-being the highest. Moreover, youth between the ages of 7 and 17 years and their caregivers scored school-related well-being the lowest. Coping strategies to deal with stressful situations differ between children and caregivers. While children mainly engage in social withdrawal, caregivers engage in cognitive restructuring and expressing emotions. However, we did not find a relationship between coping strategies and well-being perceptions. These results highlight the need to facilitate communication spaces with both families and health professionals where the voice of children is considered.