Rheumatoid arthritis (RA) is a common inflammatory disease and its treatment is largely limited by drug ineffectiveness or severe side effects. In RA progression, multiple signalling pathways, such as hypoxia-inducible factor (HIF)-1α, nuclear factor kappa B (NF-κB), and mitogen-activated protein kinase (MAPK) pathways, act synergistically to maintain the inflammatory response. To downregulate HIF-1α, NF-κB, and MAPK expression, we proposed HIF-1α siRNA-loaded calcium phosphate nanoparticles encapsulated in apolipoprotein E3-reconstituted high-density lipoprotein (HIF-CaP-rHDL) for RA therapy. Here, we evaluated the potential of CaP-rHDL nanoparticles in RA therapy using a murine macrophage line (RAW 264.7) and a collagen-induced arthritis (CIA) mouse model. The CaP-rHDL nanoparticles showed significant anti-inflammatory effects along with HIF-1α knockdown and NF-κB and MAPK signalling pathway inhibition in lipopolysaccharide-activated macrophages. Moreover, they inhibited receptor activator of NF-κB ligand (RANKL)-induced osteoclast formation. In CIA mice, their intravenous administration resulted in high accumulation at the arthritic joint sites, and HIF-CaP-rHDL effectively suppressed inflammatory cytokine secretion and relieved bone erosion, cartilage damage, and osteoclastogenesis. Thus, HIF-CaP-rHDL demonstrated great potential in RA precision therapy by inhibiting multiple inflammatory signalling pathways.