Delayed heart rate recovery (HRR) post treadmill exercise testing reflects autonomic dysfunction and is related to worse cardiovascular outcome. The present study compared HRR in normotensive subjects and hypertensive patients taking antihypertensive medications with controlled blood pressure (BP) and uncontrolled BP. A total of 279 consecutive patients with (n = 140, HP) and without (n = 139, N-HP) essential hypertension who were hospitalized in our department during May 2012 to March 2016 were included in this study. All subjects underwent treadmill exercise testing. Hypertensive patients were divided into controlled BP (n = 88) and uncontrolled BP (n = 52) groups according to their BP prior to treadmill exercise testing. Body mass index, triglyceride level and incidence of diabetes mellitus (DM) were significantly higher in the HP group than in the N-HP group, and HDL-c and HRR were significantly lower. Male gender, higher creatinine value and lower cholesterol and HDL-c were associated with lower HRR in the N-HP group, and higher triglyceride, lower LDL-c, and HDL-c were associated with lower HRR in the HP group. More frequent, ≥ 3, antihypertensive drug use, less monotherapy use and high incidence of smokers and lower HRR were found in hypertensive patients with uncontrolled BP compared to hypertensive patients with controlled BP. The present results demonstrate that uncontrolled BP following antihypertensive medication is associated with lower HRR in hypertensive patients.