This paper addresses an investigation into a leader‐following consensus problem in a novel multi‐agent‐based SIS (Susceptible‐Infected‐Susceptible) epidemic model. As infectious diseases are easily spread through travel, the model considers each agent to represent a city in an infected country, interacting with neighbouring cities towards achieving disease eradication through consensus. To make the model more realistic, the Effect Terms (ETs) arising from the effects of agent states on each other are also considered. The differential equations' positivity and existence of solutions are examined, and the proposed model's equilibrium points are obtained, with stability analysed using new local and global basic reproduction numbers defined in this study. Additionally, a leader‐following consensus control for the multi‐agent‐based system is proposed to drive each agent to follow a virtual leader agent. Finally, numerical simulations are included to validate the theoretical findings corresponding to the proposed scheme.