Five RCTs (two hundred eighty-one patients) were eligible for meta-analysis comparing polynucleotides with hyaluronic acid for intra-articular polynucleotide injections to treat knee osteoarthritis. The primary outcome of interest was pain, most commonly measured using the visual analogue scale. Secondary outcomes included functional outcome scores (Western Ontario and McMaster University Osteoarthritis Index (WOMAC), Knee injury and Osteoarthritis Outcome Score (KOOS), and Knee Society Score (KSS)) and adverse events. Outcomes were assessed between one and four months for the primary meta-analysis, with selected studies reporting longer follow-up. Overall, the results of the study revealed significantly greater pain reduction with polynucleotides compared with hyaluronic acid at two months, with superior functional outcomes at similar time points. In conclusion, intra-articular polynucleotide injections appear to provide superior short-term pain relief and modest functional improvement compared with hyaluronic acid, with a comparable safety profile.