Using a classical example, the Lorenz‐63 model, an original stochastic framework is applied to represent large‐scale geophysical flow dynamics. Rigorously derived from a reformulated material derivative, the proposed framework encompasses several meaningful mechanisms to model geophysical flows. The slightly compressible set‐up, as treated in the Boussinesq approximation, yields a stochastic transport equation for the density and other related thermodynamical variables. Coupled to the momentum equation through a forcing term, the resulting stochastic Lorenz‐63 model is derived consistently. Based on such a reformulated model, the pertinence of this large‐scale stochastic approach is demonstrated over classical eddy‐viscosity based large‐scale representations.