Autologous hematopoietic stem cell transplantation (AHSCT) is associated with sexual dysfunction and hypogonadism. Androgens are associated with sexual function in healthy men, but the role of estrogens is less well-known, and the association of these sex steroids with sexual function during AHSCT has not been characterized. The purpose of this study was to determine the predictive value of sex hormones before and acutely after AHSCT on sexual function recovery. We examined sex hormones and self-reported sexual function before (PRE) and 1-month post-AHSCT (MONTH1; n = 19), and sexual function again 1-year post-AHSCT in men (YEAR1; n = 15). Sexual function decreased from PRE to MONTH1 (p ≤ 0.05) with no differences between PRE and YEAR1. Erectile dysfunction was prevalent at PRE (68.4%) and increased at MONTH1 (100%; p ≤ 0.05) but was not different between PRE and YEAR1 (60.0%). From PRE to MONTH1, total testosterone (TT), dihydrotestosterone (DHT), follicle-stimulating hormone, and sex-hormone-binding globulin (SHBG) increased (p ≤ 0.02) while estradiol (p ≤ 0.026) and estrone decreased (p ≤ 0.001). MONTH1 TT and DHT were associated with sexual function at MONTH1, while PRE SHBG, MONTH1 estradiol, and change in estrone predicted sexual function at YEAR1. Sexual dysfunction is very prevalent prior to AHSCT and is transiently and severely worsened acutely after. AHSCT induces acute decreases in total and free estrogens, with SHBG increases leading to increases in total androgens, without changes in free androgens. Androgens and estrogens are both adversely affected by AHSCT but may predict sexual dysfunction in this population. This supports the premise that estrogen impacts sexual function independent from androgens and that steroid hormones are associated with acute changes in sexual function in this setting. Larger, controlled trials with long-term sex hormone assessment will need to confirm the association between early changes in estrogens and long-term sexual function recovery.