Otitis media (OM) is a frequent disease with incidence rate of 5300 cases per 100,000 people. Recent studies showed that polymicrobial biofilm formation represents a significant pathogenic mechanism in recurrent and chronic forms of OM. Biofilm enables bacteria to resist antibiotics that would typically be recommended in guidelines, contributing to the ineffectiveness of current antimicrobial strategies. Given the challenges of successfully treating bacterial biofilms, there is an growing interest in identifying novel and effective compounds to overcome antibacterial resistance. The objective of this review was to provide an overview of the novel compounds with antibiofilm effects on bacterial biofilm formed by clinical isolates of OM. The systematic review included studies that evaluated antibiofilm effect of novel natural or synthetic compounds on bacterial biofilm formed from clinical isolates obtained from patients with OM. The eligibility criteria were defined using the PICOS system: (P) Population: all human patients with bacterial OM; (I) Intervention: novel natural or synthetic compound with biofilm effect; (C) Control standard therapeutic antimicrobial agents or untreated biofilms, (O) Outcome: antibiofilm effect (biofilm inhibition, biofilm eradication), (S) Study design. The PRISMA protocol for systematic reviews and meta-analysis was followed. From 3564 potentially eligible studies, 1817 duplicates were removed, and 1705 were excluded according to defined exclusion criteria. A total of 41 studies with available full texts were retrieved by two independent authors. Fifteen articles were selected for inclusion in the systematic review which included 125 patients with OM. A total of 17 different novel compounds were examined, including N-acetyl-L-cysteine (NAC), tea tree oil, xylitol, eugenol, Aloe barbadensis, Zingiber officinale, Curcuma longa, Acacia arabica, antisense peptide nucleic acids, probiotics Streptococcus salivarius and Streptococcus oralis, Sodium 2-mercaptoethanesulfonate (MESNA), bioactive glass, green synthesized copper oxide nanoparticles, radish, silver nanoparticles and acetic acid. Staphylococcus aureus was the most commonly studied pathogen, followed by Pseudomonas aeruginosa and Haemophilus influenzae. Biofilm inhibition only by an examined compound was assessed in six studies; biofilm eradication in four studies, and both biofilm inhibition and biofilm eradication were examined in five studies. This systematic review indicates that some compounds like NAC, prebiotics, nanoparticles and MESNA that have significant effects on biofilm are safe and could be researched more extensively for further clinical use. However, a lack of data about reliable and efficient compounds used in therapy of different types of otitis media still remains in the literature.