The formation and acceleration of a relativistic fireball, the initial condition for gamma-ray bursts (GRBs), occur below the photosphere and cannot be directly observed through electromagnetic waves, leaving the process largely unknown. Since the fireball forms from high-density matter near a black hole, neutrons are injected in nearly equal amounts to protons. While neutrons interact with protons via nuclear forces, protons also interact with magnetic fields, photons, and electrons via electromagnetic forces. This leads to a significant relative velocity between neutrons and protons, causing inelastic collisions that produce GeV-TeV neutrinos (Bahcall & Meszaros, 2000). These neutrinos from the sub-photosphere can be messengers, which tell when, where, and how baryons (protons and neutrons) are injected into the fireball and how it expands and accelerates. Using neutron-inclusive shell simulations with initial conditions based on the collapsar scenario, we link the statistical inhomogeneity of the jet at the breakout of the progenitor to the dissipation that occurs inside and outside the photosphere, and calculate the GeV–TeV neutrino counterpart originated from inelastic neutron-proton interactions consistently with the prompt gamma-ray emission. Our result suggests that GRBs with relatively low gamma-ray luminosities, as well as X-ray-rich transients, can be promising targets for ongoing and future GeV–TeV neutrino transient searches.