The phenolic acid and flavonoid contents of Malaysian Tualang, Gelam, and Borneo tropical honeys were compared to those of Manuka honey. Ferric reducing/antioxidant power assay (FRAP) and the 1,1‐diphenyl‐2‐picryl‐hydrazyl (DPPH) radical‐scavenging activities were also quantified. All honey extracts exhibited high phenolic contents (15.21 ± 0.51– 42.23 ± 0.64 mg/kg), flavonoid contents (11.52 ± 0.27– 25.31 ± 0.37 mg/kg), FRAP values (892.15 ± 4.97– 363.38 ± 10.57 μM Fe[II]/kg), and high IC₅₀ of DPPH radical‐scavenging activities (5.24 ± 0.40– 17.51 ± 0.51 mg/mL). Total of 6 phenolic acids (gallic, syringic, benzoic, trans‐cinnamic, p‐coumaric, and caffeic acids) and 5 flavonoids (catechin, kaempferol, naringenin, luteolin, and apigenin) were identified. Among the Malaysian honey samples, Tualang honey had the highest contents of phenolics, and flavonoids, and DPPH radical‐scavenging activities. We conclude that among Malaysian honey samples, Tualang honey is the richest in phenolic acids, and flavonoid compounds, which have strong free radical‐scavenging activities.