Biofunctionalized ferrofluid droplets carrying a measured volume of analytes or reagents can be manipulated magnetically on a flat microfluidic platform, executing key tasks of a micrototal analysis system (µ-TAS). Precise control of these ferrofluid droplets can be achieved using on-chip miniaturized magnetic coils which require delicate combination of operating parameters, e.g., magnetizing current and timing of switching, fluid viscosity, droplet size, etc. Herein we present a proof of concept demonstration of magnetic manipulation of an immiscible, microliter-scale ferrofluid droplet over a thin aqueous film on a solid substrate, using an array of square electromagnets. The droplet can be moved in a zigzag or a less meandering path over an active substrate area by sequential switching of the electromagnet array with adjusting the operating parameters, e.g., fluid viscosity, current in the coil, and the droplet volume. The transport is broadly classified into a viscosity-dominated regime and an inertia-influenced one. Transport time of the droplet for the viscous regime is expressed in terms of a generalized group-variable involving the operating parameters. This magnetically manipulated ferrofluid droplets handling system offers a promising tool for miniscule sample handling in lab-on-chip devices.