The occurrence of multidrug-resistant or meticillin-resistant Staphylococcus aureus (MRSA) has become an important issue in clinics. This study evaluated a combinatorial treatment approach by using the well-documented antibacterial protein apo-bovine lactoferrin (apo-bLf) or its hydrolysate and specific probiotic supernatants for controlling MRSA infection. Clinical MRSA strains were isolated from different patient specimens. Apo-bLf-hydrolysate possessed stronger anti-MRSA activity than complete bLf in that it inhibited the growth of most MRSA strains tested in vitro. Otherwise, the supernatants produced by Lactobacillus fermentum (ATCC 11739), Bifidobacterium longum subsp. longum (ATCC 15707) and Bifidobacterium animalis subsp. lactis (BCRC 17394) inhibited the growth of various MRSA strains. Further, L. fermentum or B. animalis subsp. lactis supernatant plus apo-bLf or bLf-hydrolysate led to partially synergistic to synergistic growth-inhibitory activity against MRSA strains. However, L. fermentum and not B. animalis subsp. lactis or B. longum subsp. longum was observed to resist the antibacterial activity of both apo-Lf and bLf-hydrolysate. Therefore, it is suggested that L. fermentum could be the best candidate to be used with apo-bLf or bLf-hydrolysate as a live supplement against MRSA infections.