Nonrelativistic Quantum Chromodynamics (NRQCD) breaks down in the region of low transverse momentum, where the transverse momentum of the produced quarkonium state is sensitive to multiple scattering with the incoming hadron and to soft gluon radiation. In this kinematic regime, the transverse-momentum-dependent (TMD) factorization framework is required, promoting the long-distance matrix elements (LDMEs) of NRQCD to the so-called TMD shape functions (TMDShFs), which encode both the soft gluon radiation and the formation of the heavy-quark bound state. In this work, we apply an effective-field theory approach (combining NRQCD and SCET) to the photon-gluon fusion process in inclusive J/ψ leptoproduction. We derive a factorization theorem for the cross section in terms of TMDShFs, compute these quantities at next-to-leading order, establish their evolution, and study their matching onto the corresponding LDMEs in the high-transverse-momentum region. Our results are particularly relevant to the Electron-Ion Collider, where J/ψ leptoproduction can be used to probe gluon transverse-momentum-dependent parton distribution functions (gluon TMDPDFs).