Background and Aims Penguins are seabirds that manifest physiological and immunological alterations during the reproductive season. The objectives of this study were to evaluate the laboratory parameters of male and female Magellanic penguins and to determine the penguins' hematological response to homeopathic medicines during that reproductive period. Methods Penguins (N = 18), kept under human care in a zoological park setting, were evaluated during the reproductive period and were divided randomly into two groups: a group subjected to treatment with Echinacea angustifolia 6cH and Avena sativa 6cH (N = 8; four breeding couples), and a placebo control group (N = 10; five breeding couples). The investigators were blinded to treatment allocation. Two-way ANOVA was performed to determine whether the experimental group (control or verum) and the sex of the animal had any significant effect on the variation of each hematological parameter between the samples. One-way ANOVA was performed on hematological parameters for which the sex did not present a significant effect. The significance level was p ≤0.05. Results Significant effects were seen regarding the following: mean corpuscular volume (MCV), in which the verum group showed an increase (29.78 ± 52.95 fL) while the control group showed stability/reduction (−3.08 ± 46.36 fL) (p = 0.049); proportion of heterophils, in which the verum group showed a less marked increase (8.38 ± 12.53%) than that of the control group (18.00 ± 9.37%) (p = 0.010); lymphocyte concentration, in which the verum group showed less marked reduction (−4.39 ± 2.21 × 109 cells/L) than that of the control group (−1.56 ± 2.76 × 109 cells/L) (p = 0.001); and proportion of lymphocytes, in which the verum group showed a less marked reduction (−6.75 ± 10.35%) than that of the control group (−17.3 ± 8.73%) (p = 0.002). Conclusion Comparison of samples collected before and during the reproductive period showed that, regardless of group allocation, there were differences in the effects on MCV, heterophils and lymphocytes. Treatment with Echinacea angustifolia and Avena sativa resulted in maintenance of lymphocyte levels in Magellanic penguins during the breeding period, thus aiding these birds' immunity.