(1) Background: Cephalosporins (CA) are the first-line antibiotic prophylaxis recommended to prevent surgical site infection (SSI) after cardiac surgery. The combination of vancomycin/gentamicin (VGA) might represent a good alternative, but few studies have evaluated its efficacy in SSI prevention. (2) Methods: A single-centre retrospective study was conducted over a 13-year period in all consecutive adult patients undergoing elective cardiac surgery. Patients were stratified according to the type of antibiotic prophylaxis. CA served as the first-line prophylaxis, and VGA was used as the second-line prophylaxis. The primary endpoint was SSI occurrence at 90 days, which was defined as the need for reoperation due to SSI. (3) Results: In total, 14,960 adult patients treated consecutively from 2006 to 2019 were included in this study, of whom 1774 (12%) received VGA and 540 (3.7%) developed SSI. VGA patients had higher severity with increased 90-day mortality. Nevertheless, the frequency of SSI was similar between CA and VGA patients. However, the microbiological aetiologies were different, with more Gram-negative bacteria noted in the VGA group. (4) Conclusions: VGA seems to be as effective as CA in preventing SSI.