Although accumulating evidence suggests the benefits of cardiorespiratory fitness and muscular fitness, little knowledge exists on how other physical fitness (PF) components are associated with cardiovascular disease (CVD) risk markers in children. Additionally, much of the relevant evidence is from longitudinal studies with CVD risk markers at a single time point (i.e., baseline) rather than changes in PF. The purpose of the present study was to examine whether initial 1-year changes in different performance measures of PF (i.e., endurance performance, muscular strength/endurance, flexibility, agility, and speed) can predict the subsequent changes (2-year change) in blood lipid concentrations in children. This 2-year longitudinal study included a total of 251 Japanese children (mean age 9.2 ± 0.4). PF tests were performed to comprehensively evaluate the participant’s fitness levels (handgrip strength [upper body muscular strength], bent-leg sit-ups [muscular endurance], sit-and-reach [flexibility], side-step [agility], 20-meter shuttle run [endurance performance], 50-meter sprint [speed], standing long jump [lower body muscular strength], and softball throw [explosive arm strength and throwing ability]). Fasting lipid profile was assayed for triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and non-HDL-C concentration. Multilevel linear regressions were used to examine the associations between the preceding changes (over 1-year) in PF and subsequent changes (over 2-years) in blood lipid concentrations. We also examined the simultaneous associations between 2-year changes in PF and 2-year changes in blood lipid concentrations. For boys, preceding improvement in handgrip strength was negatively associated with TG concentration (β = -0.260, p = 0.030); improvements in bent-leg sit-ups were negatively associated with clustered lipid scores (β = -0.301, p = 0.038) and non-HDL-C (β = -0.310, p = 0.044); and improvements in 50m sprinting were associated with subsequent changes in non-HDL-C (β = 0.348, p = 0.006) and LDL-C (β = 0.408, p = 0.001). For girls, improvements in handgrip strength was negatively associated with TG concentration (β = -0.306, p = 0.017); and improvements in standing long jump were negatively associated with non-HDL-C (β = -0.269, p = 0.021) and LDL-C (β = -0.275, p = 0.019). For boys and girls, there were no significant simultaneous associations between 2-year changes in PF and 2-year changes in blood lipid concentrations. In conclusion, preceding change in physical fitness in relation to change in blood lipid concentration likely reflect a physiological adaptation to growth and maturation since these associations diminished in the subsequent year.