Tsigos et al., [1] investigated neuroendocrine factors and stress factors in Hypothalamic–pituitary–adrenal axis problems. Savic and Jelic [2] performed a theoretical study of hypothalamo-pituitary adrenocortical axis dynamics. Jelic et al., [3] mathematically modelled the hypothalamic–pituitary–adrenal system activity. Lenbury et al., [4] developed a delay-differential equation model of the feedback-controlled hypothalamus-pituitary-adrenal axis in humans. Kyrylov et al., [5] modelled the oscillatory behavior of the hypothalamic-pituitary-adrenal axis. Savic et al., [6] discussed the stability of a general delay differential model of the hypothalamo-pituitary-adrenocortical system. Smith et al., [7] studied the role of the hypothalamic–pituitary–adrenal axis in neuroendocrine responses to stress. Gupta et al., [8] showed that the inclusion of the glucocorticoid receptor in a hypothalamic pituitary adrenal axis model reveals bistability. Bairagi et al., [9] discussed the variability in the secretion of corticotropin-releasing hormone, adrenocorticotropic hormone and cortisol and understandability of the hypothalamic-pituitary-adrenal axis dynamics. Vinther et al., [10] developed a minimal model of the hypothalamic-pituitary-adrenal axis. Jelic et al., [11] discussed the predictive modeling of the hypothalamic-pituitary-adrenal (HPA) function. Markovic et al., [12], performed predictive modeling studies of the hypothalamic-pituitary-adrenal (HPA) axis response to acute and chronic stress. Markovic et al., [13] investigated, the stability of the extended model of the hypothalamic-pituitary-adrenal axis examined by stoichiometric network analysis. Andersen et al., [14] performed mathematical modeling studies of the hypothalamic-pituitary-adrenal gland (HPA) axis, including hippocampal mechanisms. Postnova et al., [15] developed a minimal physiologically based model of the HPA axis under influence of the sleep-wake cycles. Gudmand-Hoeyer et al., [16] performed a Patient-specific modeling of the neuroendocrine HPA-axis and studied its relation to depression. Hosseinichimeh et al., [17] performed additional modeling the hypothalamus-pituitary-adrenal axis. Malek et al., [18] discussed the dynamics of the HPA axis and inflammatory cytokines. Markovic et al., [19] investigated the cholesterol effects on the dynamics of the hypothalamic-pituitary–adrenal (HPA) axis. Cupic et al., [20] studied the dynamic transitions in a model of the hypothalamic–pituitary–adrenal axis. Pierre et al., [21] investigated the role of the hypothalamic-pituitary-adrenal axis in modulating seasonal changes in immunity. Abulseoud et al., [22] demonstrated the existence of corticosterone oscillations during mania induction in the lateral hypothalamic kindled rat-Experimental observations. Stanojevic et al., [23] performed kinetic modelling of testosterone-related differences in the hypothalamic-pituitary-adrenal axis response to stress. Bangsgaard et al., [24] performed patient-specific modelling studies of the HPA axis related to the clinical diagnosis of depression. Kim et al., [25] performed mathematical modeling to improve diagnosis of post-traumatic and related stress disorders by perturbing the hypothalamic-pituitary-adrenal stress response system. Stanojevic et al., [26] modelled the hypothalamic-pituitary-adrenal axis perturbations by externally induced cholesterol pulses of finite duration and with asymmetrically distributed concentration profiles. Kim LU et al., [27] perturbed the hypothalamic pituitary–adrenal axis and developed a mathematical model for interpreting PTSD assessment tests. Comput Psychiatry 2017, 2: 28-49. Kaslik et al., [28] discussed the stability and demonstrated the existence of Hopf bifurcations for the hypothalamic-pituitary-adrenal axis model with memory. The aim of this paper is to (1) perform bifurcation studies on the hypothalamic–pituitary–adrenal axis model described in Cupic et al., [20], demonstrate the existence of Hopf bifurcations and provide a strategy to eliminate them and (2) to perform multiobjective nonlinear model predictive control calculations on the same hypothalamic-pituitary–adrenal axis model. This document is organized as follows. The model equations for the hypothalamic-pituitary-adrenal axis model Cupic et al., [20] is first described. This is followed by a description of the numerical methods (bifurcation analysis and MNLMPC). The results and discussion are then presented, followed by the conclusions.