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We report on the electronic, magnetic, and magneto-transport properties of Fe-based kagome Dirac system, RFe$_6$Sn$_6$ (R = Ho, Dy). Magnetic properties study reveals an antiferromagnetic order with N$\acute{e}$el temperature of $T_N \approx$ 570 K. Additionally, a weak ferromagnetic order emerge at low temperatures. Magnetotransport measurements demonstrate an extremely large magnetoresistance (XMR) reaching as high as $3\times 10^{3} \%$ for HoFe$_6$Sn$_6$ and $ 1\times 10^{3} \%$ for DyFe$_6$Sn$_6$ when measured at 2 K with 9 T of magnetic field. The semi-classical two-band model fitting of the Hall conductivity reveals nearly perfect electron-hole compensation and high carrier mobility, which leads to XMR behaviour in these system. Further, we identify large magnetoresistance anisotropy for the magnetic fields applied in different crystallographic orientations. In addition, considerable modification in the angle-dependent magnetoresistance (ADMR) pattern has been noticed between 2 and 50 K, indicating temperature-dependent changes in the Fermi surface topology of these systems.