Non-Hermitian systems have garnered significant attention due to the emergence of novel topology of complex spectra and skin modes. However, investigating transport phenomena in such systems faces obstacles stemming from the non-unitary nature of time evolution. Here, we establish the continuity equation for a general non-Hermitian Hamiltonian in the Schr\"odinger picture. It attributes the universal non-conservativity to the anti-commutation relationship between particle number and non-Hermitian terms. Our work derives a comprehensive current formula for non-Hermitian systems using Green's function, applicable to both time-dependent and steady-state responses. To demonstrate the validity of our approach, we calculate the local current in models with one-dimensional and two-dimensional settings, incorporating scattering potentials. The spatial distribution of local current highlights the widespread non-Hermitian phenomena, including skin modes, non-reciprocal quantum dots, and corner states. Our findings offer valuable insights for advancing theoretical and experimental research in the transport of non-Hermitian systems.