Little research has been published assessing changes in the functional health status of children and adolescents with chronic kidney disease (CKD). We know little about which clinical parameters influence functional status or health-related quality of life in these young people. In a prospective study using data from semi-annual visits over a 4-year period from 78 adolescents with CKD aged 11 years to 18 years, we detail the impact of several clinical measures (i.e., kidney function, albumin, hematocrit, height) on short-term changes in health-related quality of life. The 50-item Child Health Questionnaire Parent Form, a validated health-related quality of life measure in children, was used to obtain physical and psychosocial functioning summary scores at each visit. After adjustment for the variables mentioned above, the physical summary score on the Child Health Questionnaire (CHQ) declined as glomerular filtration rate declined. Increasing height was associated with a positive change in physical and psychosocial summary scores. We conclude that decline in kidney function is associated with a subsequent decline in health-related quality of life, particularly in terms of physical activity.