Ferrofluids can be conveniently used in magnetic immune-assay techniques, such as magnetic labeling, magnetic drug targeting, hyperthermia, contrast enhancement for magnetic resonance imaging, and magnetic separation of cells. A main issue of immune-assay techniques, often adopted in lab-on-chip systems, is the transitions of the biotarget from one site to another site. This is mandatory to expose the biotarget linked to the carrier to the chemical/physical processes occurring in different sites of the system. In this paper, a strategy to control and to monitor the position of a ferrofluid mass, which can assume the role of carrier, along a predefined path is presented together with some experimental results. The behavior of the sensing readout strategy for different masses of ferrofluid, the selected path, and the time of residence of the ferrofluid carrier in each site has been investigated. A minimum residence time of 740 ms has been estimated for the LabScale prototype developed, which confirms the suitability of the proposed control and sensing strategy. Moreover, the possibility to detect the direction of the ferrofluid mass movement has been demonstrated.