Background Inflammation plays a significant role in the pathogenesis of knee osteoarthritis (KOA). Although both Electro-acupuncture (EA) and Manual Acupuncture (MA) are known to influence systemic inflammation, little is known about the potential changes in inflammation as a working mechanism of EA and MA in KOA.Methods Data from the Acupuncture for Knee Osteoarthritis Trial (ATKOA) were used. Serum concentrations of inflammatory factors (tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), IL-6, IL-8, IL-18, IL-4, IL-10,IL-13,IL-15, IL-17, monocyte chemotactic protein-1 (MCP-1), CCchemokine ligand 5 (CCL5), and cartilage degradation biomarkers (matrix metalloproteinase-1 MMP-1, MMP-3, MMP-13 and cartilage oligomeric matrix protein COMP) were measured at baseline and after 8 weeks of treatment. Clinical outcomes were valid and reliable self-reported pain and function measures for osteoarthritis using the Western Ontario and McMasters osteoarthritis index questionnaire (WOMAC) and Visual Analogue Scale (VAS) at baseline and post-treatment.Results Both 8-weeks EA and MA significantly reduced pro-inflammatory cytokines (TNFα, IL-1β) and cartilage degradation biomarkers (MMP-3, MMP-13), significantly increased the anti-inflammatory cytokine IL-13 compared with pre-treatment (p<0.05). Further, the reduction of TNF-α were more significant in EA when compared to MA (p=0.046). While, there was no significant difference between groups in cytokines IL-1β (p=0.102), MMP-3(p=0.113), MMP-13(p=0.623) or IL-13(p=0.935). Moreover, in both EA and MA the effect of acupuncture on the VAS and WOMAC function scale after 8 weeks is clinically important, although no significant differences were found between groups.Conclusions 8 weeks of both EA and MA seem to provide improvement in pain relief and function among individuals with mild to moderate knee OA. This benefit is partly mediated by changes of major inflammatory factors TNF-α, IL-1β and IL-13.