Brain damage (stroke, trauma, hypoperfusion) is accompanied not only by neurological disorders but also by endocrine deficiency. It may manifest in different forms, ranging from barely noticeable to those that radically alter life, affecting the regulation of metabolism, sexual health, psychological well-being, and rehabilitation potential. To assess the atrophy of the endocrine apparatus of the testes under cerebral hypoperfusion in rats and the possibility of its pharmacological correction. Cerebral hypoperfusion in rats was modeled by bilateral common carotid artery occlusion (BCCAO). Atrophic changes in the testicular interstitium and the effects of clomiphene and metformin on their course were studied. Clomiphene, as an activator of the hypothalamic–pituitary–testicular axis, exhibited these properties also under severe chronic cerebral hypoperfusion in rats and prevented/restored the morphofunctional state of the endocrine apparatus of the testes. Metformin showed a tendency toward depression of the testicular endocrine apparatus in intact animals. At later stages of cerebral hypoperfusion in rats, it may have improved the condition of Leydig cells by compensating for progressively accumulating metabolic disturbances. Combined administration of clomiphene and metformin under cerebral hypoperfusion demonstrated lower effectiveness in restoring the morphofunctional state of the testicular endocrine apparatus compared to clomiphene alone. Considering the latter, it is necessary to correlate the results of testicular changes with the reduction of neurological symptoms that develop under cerebral hypoperfusion during the action of clomiphene and metformin, to conclude the expediency of correcting the observed alterations. Cerebral hypoperfusion leads to atrophic changes in the endocrine apparatus of the testes. By causing a decrease in testosterone production, this may reduce the effectiveness of compensatory and recovery processes. Clomiphene was shown to be a promising drug for correcting atrophic changes in the testicular endocrine apparatus under chronic cerebral hypoperfusion. In contrast, metformin demonstrated lower/negative effectiveness in this direction, and its combined administration was less effective than clomiphene alone.