Background/Objectives: Unexplained infertility is a worldwide problem affecting a significant proportion of couples of reproductive age. Recent studies suggest that alterations in the vaginal microbiota are related to female infertility, while supplementation with some probiotic strains has been shown to improve pregnancy rates in couples experiencing this problem. This study aimed to evaluate the impact of oral administration of Ligilactobacillus salivarius CECT5713 on pregnancy success rates in couples with unexplained infertility prior to in vitro fertilization (IVF). Methods: Seventy couples were randomized to receive either a placebo or a probiotic intervention (one capsule per day containing an excipient only or 3 × 10⁹ viable cells of L. salivarius CECT5713 plus an excipient, respectively); 57 couples completed the study. Baseline data on demographics, health status (including gynecological and reproductive history), and lifestyle habits were collected. Vaginal swabs and semen samples were obtained from each couple before the intervention and immediately prior to IVF or upon confirmed pregnancy and were analyzed for microbiological (using both culture-dependent and -independent methods) and immunological profiles. Results: Oral administration of L. salivarius CECT5713 in couples with unexplained infertility scheduled for IVF resulted in a significantly higher pregnancy success rate (48.1%) compared to the placebo group (20.0%) (one-tailed Chi-square test; p < 0.024). The probiotic intervention improved both vaginal and semen immunological profiles, with no substantial changes observed in their microbial composition. Conclusions: These preliminary findings support the potential of L. salivarius CECT5713 supplementation to enhance fertility outcomes in couples with unexplained infertility.