The relationship between non-communicable diseases (NCDs) and eating behaviour has long been attributed to a surplus of food and energy. However, the increase in the prevalence of NCDs and their underlying low-grade inflammatory milieu among people of low socioeconomic status (SES) has highlighted the existence of a confounding factor. In this work, we aim to study the effect of lysine deficiency on some inflammatory markers in the absence or presence of an inflammatory insult [lipopolysaccharide (LPS)]. For this purpose, thirty-two five-week-old male Sprague Dawley rats were randomly distributed into four groups: 1) control diet, 2) control diet+LPS, 3) lysine-deficient diet, and 4) lysine-deficient diet+LPS. Groups were only allowed their experimental diets for four weeks, during which LPS (50 µg/kg) or saline injections were administered intraperitoneally three times per week. The study showed that lysine deficiency blunted growth and body compartments development, decreased albumin production and elevated liver c-reactive protein (CRP) expression, independently of interleukins 6 and 1β, the main precursors of CRP. Also, the insufficient levels of lysine in the diet increased hyperactivity and triggered an anxiety-like behaviour, exacerbated with LPS. This work presents evidence that various physiological changes are associated with the absence of a sufficient amount of lysine in the diet and can potentially increase the risk factor for diseases. Thus, the increment in NCDs among the low SES populations, who heavily rely on cereals as a main source of protein, can be, at least partially, blamed on low lysine availability in diets.