The main goal of the paper is to present and study models of multi-agent systems for which the dynamics of the agents are described by a Caputo fractional derivative of variable order and a kernel that depends on an increasing function. Also, the order of the fractional derivative changes at update times. We study a case for which the exchanged information between agents occurs only at initially given update times. Two types of linear variable-order Caputo fractional models are studied. We consider both multi-agent systems without a leader and multi-agent systems with a leader. In the case of multi-agent systems without a leader, two types of models are studied. The main difference between the models is the fractional derivative describing the dynamics of agents. In the first one, a Caputo fractional derivative with respect to another function and with a continuous variable order is applied. In the second one, the applied fractional derivative changes its constant order at each update time. Mittag–Leffler stability via impulsive control is defined, and sufficient conditions are obtained. In the case of the presence of a leader in the multi-agent system, the dynamic of the agents is described by a Caputo fractional derivative with respect to an increasing function and with a constant order that changes at each update time. The leader-following consensus via impulsive control is defined, and sufficient conditions are derived. The theoretical results are illustrated with examples. We show with an example the leader’s influence on the consensus.