Manganese (Mn) is a key Fe-group elements, commonly employed in stellar population and nucleosynthesis studies to explore the role of SN Ia. We have developed a new non-local thermodynamic equilibrium (NLTE) model of Mn, including new photo-ionisation cross-sections and new transition rates caused by collisions with H and H- atoms. We applied the model in combination with 1-dimensional (1D) LTE model atmospheres and 3D hydrodynamical simulations of stellar convection to quantify the impact of NLTE and convection on the line formation. We show that the effects of NLTE are present in Mn I and, to a lesser degree, in Mn II lines, and these increase with metallicity and with effective temperature of a model. Employing 3D NLTE radiative transfer, we derive new abundance of Mn in the Sun, A(Mn)=5.52 +/- 0.03 dex, consistent with the element abundance in C I meteorites. We also apply our methods to the analysis of three metal-poor benchmark stars. We find that 3D NLTE abundances are significantly higher than 1D LTE. For dwarfs, the differences between 1D NLTE and 3D NLTE abundances are typically within 0.15 dex, however, the effects are much larger in the atmospheres of giants owing to their more vigorous convection. We show that 3D NLTE successfully solves the ionisation and excitation balance for the RGB star HD 122563 that cannot be achieved by 1D LTE or 1D NLTE modelling. For HD 84937 and HD 140283, the ionisation balance is satisfied, however, the resonance Mn I triplet lines still show somewhat lower abundances compared to the high-excitation lines. Our results for the benchmark stars confirm that 1D LTE modelling leads to significant systematic biases in Mn abundances across the full wavelength range from the blue to the IR. We also produce a list of Mn lines that are not significantly biased by 3D and can be reliably, within the 0.1 dex uncertainty, modelled in 1D NLTE.