•Advection reaction susceptible infected recovered (SIR) epidemic model with relapse and immunity loss is considered for numerical analysis in which state variables represent the population sizes.•Positivity preserving numerical technique is designed for the epidemic model as state variables are taken in absolute.•The proposed scheme preserves all the important properties possessed by continuous SIR epidemic model.•M-matrix theory is used to prove the positivity of the proposed technique.•Numerical simulations are presented to verify all the attributes of the proposed numerical schemes. Background and objective: Epidemic models are used to describe the dynamics of population densities or population sizes under suitable physical conditions. In view that population densities and sizes cannot take on negative values, the positive character of those quantities is an important feature that must be taken into account both analytically and numerically. In particular, susceptible-infected-recovered (SIR) models must also take into account the positivity of the solutions. Unfortunately, many existing schemes to study SIR models do not take into account this relevant feature. As a consequence, the numerical solutions for these systems may exhibit the presence of negative population values. Nowadays, positivity (and, ultimately, boundedness) is an important characteristic sought for in numerical techniques to solve partial differential equations describing epidemic models. Method: In this work, we will develop and analyze a positivity-preserving nonstandard implicit finite-difference scheme to solve an advection-reaction nonlinear epidemic model. More concretely, this discrete model has been proposed to approximate consistently the solutions of a spatio-temporal nonlinear advective dynamical system arising in many infectious disease phenomena. Results: The proposed scheme is capable of guaranteeing the positivity of the approximations. Moreover, we show that the numerical scheme is consistent, stable and convergent. Additionally, our finite-difference method is capable of preserving the endemic and the disease-free equilibrium points. Moreover, we will establish that our methodology is stable in the sense of von Neumann. Conclusion: Comparisons with existing techniques show that the technique proposed in this work is a reliable and efficient structure-preserving numerical model. In summary, the present approach is a structure-preserving and efficient numerical technique which is easy to implement in any scientific language by any scientist with minimal knowledge on scientific programming.