Background: Numerous studies have investigated links between body mass index (BMI) trajectories and cardiovascular risk, yet discrepancies in BMI measurement duration and timing of the cardiovascular-related outcome evaluation have led to inconsistent findings. Methods: We included participants from the Swedish birth cohort (BAMSE) and applied latent class mixture modeling to identify BMI trajectories using data of multiple BMI measures (≥ 4 times) from birth until 24-year follow-up (n = 3204). Subsequently, we analyzed the associations of BMI trajectories with lipids (n = 1974), blood pressure (n = 2022), HbA1c (n = 941), and blood leukocytes (n = 1973) using linear regression. We also investigated the circulating levels of 92 inflammation-related proteins (n = 1866) across BMI trajectories. Results: Six distinct BMI groups were identified, denoted as increasing—persistent high (n = 74; 2.3%), high—accelerated increasing (n = 209; 6.5%), increasing—accelerated resolving (n = 142; 4.4%), normal—above normal (n = 721; 22.5%), stable normal (n = 1608; 50.2%), and decreasing—persistent low (n = 450; 14.1%) BMI groups. The increasing—persistent high and high—accelerated increasing BMI groups had higher levels of total cholesterol [mean difference (95% confidence intervals): 0.30 (0.04–0.56) and 0.16 (0.02–0.31) mmol/L], triglyceride, low-density lipoprotein, hemoglobin A1C [3.61 (2.17–5.54) and 1.18 (0.40–1.98) mmol/mol], and low-density lipoprotein/high-density lipoprotein ratios, but a lower level of high-density lipoprotein than the stable normal BMI group. These two groups also had higher leukocyte cell counts and higher circulating levels of 28 inflammation-related proteins. No increased cardiometabolic markers were observed in the increasing—accelerated resolving BMI group. Conclusions: Participants with persistently high or accelerated increasing BMI trajectories from birth to young adulthood have elevated levels of cardiometabolic risk markers at young adulthood than those with stable normal BMI. However, a raised BMI in childhood may not be inherently harmful to cardiometabolic health, provided it does not persist into adulthood.