Dyslipidemia plays an essential role in chronic kidney disease (CKD). The role of lipids and lipoproteins in the early pre-disease state of CKD in hypertensive patients is still unclear. The study aimed to evaluate the relationship between early renal dysfunction and lipid profile parameters among hypertensive patients in Kazakhstan. From April 2015 to December 2016, 800 Kazakh males and females with primary hypertension who met the inclusion criteria were included in this cross-sectional study. Data were collected on socio-demographics, lifestyle parameters, family history of cardiovascular disease, and hypertension. Additionally, Dietary Quality Score (DQS), anthropometric data, and blood pressure were recorded. Laboratory blood measurements included eGFR (estimated glomerular filtration rate), lipid profile parameters such as Apolipoprotein B, A1, HDL-C, LDL-C, and TG. We found a linear relationship between early renal dysfunction and LDL-C, Apolipoprotein B, and Apolipoprotein B/A1 ratio, which was in all cases negative and small (r = −0.27, −0.23 and −0.16, respectively). Apolipoprotein A1, HDL-C and TG have not revealed a linear relationship with GFR (r = −0.06, r = −0.06, and r = −0.045, respectively). The multicollinearity test restricted the linear model to Apolipoprotein B only. Further linear regression analysis confirmed an inverse significant linear association between eGFR and Apolipoprotein B. Age, DQS, and income appear to be positive confounding factors, significantly fitted the final model. ROC analysis had proven the predictive power of Apolipoprotein B in pre-CKD eGFR decline before and after adjustment for age, DQS and income (AUC = 0.62 and AUC = 0.77, respectively). For differentiating non-diabetic subjects with and without pre-CKD eGFR decrease, 1.05 g/L and 0.98 g/L are likely to be optimal cutoff points in males and females, respectively. These findings will help early prediction of renal dysfunction and contribute to a more accurate estimation of CVD risk.