Niacin has been investigated for its potential impact on lipid metabolism and cardiovascular health. This meta-analysis aims to systematically evaluate the effects of niacin interventions on apo A1 and apo B levels, key regulators of lipoprotein metabolism and markers of cardiovascular risk. A comprehensive search of the literature was performed on five databases of PubMed, Scopus, Web of Science, Embase and Cochrane library, from inception up to 15 July 2023. This search identified 1452 publications, from which twelve randomised controlled trials met the inclusion criteria. The intervention dosages ranged from 500 to 3000 mg/d, and the study durations spanned from 6 to 102·8 weeks. The niacin intervention demonstrated a significant reduction in apo B levels (weighted mean differences (WMD): −24·37 mg/dl, P = 0·01). Subgroup analyses indicated that intervention duration played a role, with trials of ≤ 16 weeks showing a greater reduction in apo B. Regarding apo A1, niacin significantly increased its levels (WMD: 8·23 mg/dl, P < 0·001). Subgroup analyses revealed that the beneficial effects of niacin on apo A1 were observed at a dosage of > 1500 mg/d (P < 0·001), and extended-release niacin was more effective compared with other forms (P < 0·001). According to the Begg’s regression test, no publication bias was observed in this systematic review and meta-analysis. This meta-analysis highlights niacin’s potential role in improving lipid profiles and cardiovascular health. Further well-designed clinical trials are needed to elucidate and confirm optimal dosages and durations of niacin interventions for influencing apo A1 and B.