The present study was designed to elucidate a relationship between lymphoid organs and reproductive activity in male Japanese quails (Coturnix japonica) bred in a temperate region of Pakistan (30.3753° N, 69.3451° E) in response to photoperiodic changes. The research focused primarily on the relative morphological changes in primary (thymus and bursa of Fabricius) and secondary (spleen) lymphoid organs with respect to seasonal variations in the histomorphometry of testicular tissue. For this purpose, a comparable number of clinically healthy Japanese quails were exsanguinated during active (April–May), regressive (September–October) and inactive (January–February) reproductive phases. Following an extensive gross measurement of lymphoid and reproductive organs, a histomorphometric analysis was performed on sampled tissues by employing ImageJ® software. Blood was collected for hormonal and leukocytic analysis. One-way ANOVA was used for statistical comparison. Testes had the highest parenchymal development in the active phase (80.66 ± 21.22 µm) and the lowest in the inactive phase (27.80 ± 7.22 µm). Conversely, a percentage change was evident in the sizes of primary (bursa: 61.5%, thymus: 46.9%) and secondary (spleen: 23.9%) lymphoid organs during inactive and active reproductive phases. This study demonstrated that a physiological trade-off is imperative between immune and reproductive systems for optimum survivability and reproductive performance.