Paternal exposure to high‐fat diets or individual fatty acids (FAs) including arachidonic acid (AA) modifies progeny traits by poorly understood mechanisms. Specific male reproductive system FAs may be involved in paternal inheritance, as they can modify a range of cellular components, including the epigenome. Our objective was to determine FAs in compartments of the male reproductive system that potentially affect ejaculate composition—right and left testicular interstitial fluid (TIF), vesicular gland fluid (VGF), and epididymal adipose tissue (EAT)—in mice exposed to AA or vehicle daily for 10 days (n = 9–10/group). Whole blood (WB) and interscapular brown adipose tissue (IBAT) FA profiles were used as reference. AA significantly affected only VGF FAs relative to vehicle, that is, increased and decreased levels of arachidic and docosahexaenoic acid, respectively, versus vehicle (0.28% ± 0.01% and 0.23% ± 0.03%, respectively, p = 0.049, and 2.42% ± 0.47% and 3.00% ± 0.58%, respectively, p = 0.041). AA affected distinct FAs in WB. Additionally, we uncovered AA‐dependent and AA‐independent FA laterality. Myristic acid was higher in AA‐exposed left versus right TIF (0.68% ± 0.35% and 0.60% ± 0.11%, respectively, p = 0.004). Right TIF contained higher oleic and linoleic acid and lower stearic acid than left TIF (29.01% ± 3.07% and 24.00% ± 2.18%, respectively, p = 0.005; 9.14% ± 1.88% and 7.05% ± 1.36%, respectively, p = 0.005; and 21.90% ± 2.92% and 26.01% ± 2.46%, respectively, p = 0.036), irrespective of exposure to AA. The TIF oleic/stearic acid ratio suggested higher Stearoyl‐CoA Desaturase 1 activity in the right versus the left testis (1.35 ± 0.32 and 1.00 ± 0.17, respectively, p = 1.0 × 10−4). Multitissue comparisons revealed that TIF and VGF FA profiles were distinct from WB, EAT, or IBAT counterparts, suggesting tissue‐specific FA fingerprints. In conclusion, AA modulated selected VGF long‐chain FAs that may impact on uterine inflammation and subsequent embryonic development. AA altered local FA synthesis or selective uptake, rather than eliciting passive uptake from WB. Additionally, we uncover a significant laterality of testis FAs that may result in asymmetric sperm cell phenotypes.