This study aims to perform global gonadal and sexual function assessments in systemic lupus erythematosus-related antiphospholipid syndrome (SLE-APS) patients. A cross-sectional study was conducted in ten SLE-APS male patients and 20 healthy controls. They were assessed by demographic data, clinical features, urological examination, sexual function, testicular ultrasound, seminal parameters, sperm antibodies, and hormone profile. The median of current age was similar in SLE-APS patients and controls with a higher frequency of erectile dysfunction in the former group (30 vs. 0 %, p = 0.029). The median penis circumference was significantly reduced in SLE-APS patients with erectile dysfunction compared to patients without this complication (8.17 vs. 9.14 cm, p = 0.0397). SLE-APS patients with previous arterial thrombosis had a significantly reduced median penis circumference compared to those without this complication (7.5 vs. 9.18 cm, p = 0.039). Comparing SLE-APS patients and controls, the former had a significant lower median of sperm concentration (41.1 vs. 120.06 × 106/mL, p = 0.003), percentages of sperm motility (47.25 vs. 65.42 %, p = 0.047), normal sperm forms by WHO guidelines (11 vs. 23.95 %, p = 0.002), and Kruger criteria (2.65 vs. 7.65 %, p = 0.02). Regarding seminal analysis, the medians of sperm concentration and total sperm count were significantly lower in SLE-APS patients treated with intravenous cyclophosphamide vs. those untreated with this drug (p < 0.05). Therefore, we have observed a novel association of reduced penile size with erectile dysfunction and previous arterial thrombosis in SLE-APS patients. Penis assessment should be routinely done in SLE-APS patients with fertility problems. We also identified that intravenous cyclophosphamide underlies severe sperm alterations in these patients.