Our study aimed to determine whether proatherogenic lipid profiles exist in patients with active Takayasu arteritis (TA) and assess the relationship between different lipid profiles and disease activity in TA. A total of 132 premenopausal female patients with TA and 100 sex-, age-, and body mass index-matched healthy controls were included in our study. The clinical data were collected in detail from all participants. Patients with active TA had significantly lower levels of apolipoprotein A1 (apoA1) (1.47 ± 0.30 vs. 1.99 ± 0.33 mmol/L, p < 0.001) and lower levels of high-density lipoprotein cholesterol (HDL-C) (1.23 ± 0.33 vs. 1.68 ± 0.38 mmol/L, p < 0.001) than patients with inactive TA. However, they had higher ratios of apolipoprotein B (apoB)/apoA1 (0.74 ± 0.27 vs. 0.48 ± 0.14, p < 0.001) compared with patients with inactive TA. Multiple linear regression analysis demonstrated that the apoB/apoA1 ratio was independently associated with TA activity (β = 0.38, p = 0.04). In addition, multivariate stepwise forward regression analysis showed that the apoB/apoA1 ratio was the major determinant for high-sensitivity C-reactive protein (β = 0.58, p = 0.002). Our findings indicate that patients with active TA had proatherogenic lipid profiles. In addition, the ratio of apoB to apoA1 could be used as a marker for monitoring and targeting patients with TA.