Wireless-manipulated graphite coated nanomagnets are promising candidates for minimally invasive targeted drug delivery platforms. Iron nanowires coated with graphitic shells are synthesized by template-assisted deposition. The use of porous aluminum oxide templates enables both the batch production of nanowires by electrodeposition and their subsequent conformal encapsulation in graphite using chemical vapor deposition (CVD). High quality graphitic shells are obtained when CVD conditions are optimized using acetylene as carbon feedstock at 740 °C. Interestingly, the iron nanowires transform into iron carbide during the CVD process leading to changes in magnetic properties. The graphite coated iron nanowires are precisely manipulated against a water flow (0.1 mm/s) using a magnetic field of 350 Oe and a gradient of 50 kOe m−1 in a 5-DOF magnetic manipulation system. Our approach opens new avenues for the design and synthesis of functional graphite coated nanowires that are promising for nanorobotics applications.