  We develop an effective field theory approach for the $S$-wave
quarkonium-nucleon system. We adopt a natural power counting equivalent to
Weinberg's power counting in nucleon-nucleon effective field theories and
compute the quarkonium-nucleon potential, scattering length and effective range
up to $\mathcal{O}(m^3_{\pi}/\Lambda^3_{\chi})$ accuracy, including the full
light-quark mass dependence. We compare our results with lattice QCD studies of
quarkonium-nucleon system, obtain an estimation of the leading order
quarkonium-nucleon contact term and determine the $J/\psi$ and $\eta_c$
chromopolarizabilities.
