FenGeTe2 (n = 3, 4, and 5) has recently attracted increasing attention due to its two-dimensional van der Waals characteristic and high temperature ferromagnetism, which makes promises for spintronic devices. A Fe(1) split site is an important structural characteristic of Fe5GeTe2, which makes it very different from other FenGeTe2 (n = 3 and 4) systems. The local atomic disorder and short-range order can be induced by the split site. In this work, high-quality van der Waals ferromagnet Fe5GeTe2 single crystals were grown to study low-temperature transport properties. We found a resistivity upturn below 10 K. The temperature and magnetic field dependence of the resistivity are in good agreement with a combination of the theory of disorder-enhanced three-dimensional electron–electron and single-channel Kondo effect. The Kondo effect exists only at low magnetic fields B<3 T, while electron–electron interaction dominates the appearance for the low-temperature resistivity upturn. We believe that the enhanced three-dimensional electron–electron interaction in this system is induced by the local atomic structural disorder due to the split site of Fe(1). Our results indicate that the split site of Fe plays an important role for the exceptional transport properties.