We report on electrical, magnetic, and thermal properties of EuB5.99C0.01. The observed anomalously large negative magnetoresistance is attributed to the effect of fluctuations in carbon concentration. In accordance with our interpretation, in the bulk ferromagnetic (FM) state the carbon-rich regions give rise to helimagnetic domains, which are responsible for an additional scattering term in the electrical resistivity. Above the temperature of the bulk FM ordering, TC=4.3 K, we suppose that the carbon-rich regions act as “spacers” preventing magnetic polarons (MPs) to link, to form FM clusters, and eventually to percolate. As we propose, such spacers, being in fact volumes incompatible with the existence of MPs (and FM state in general), may be responsible for a decrease in the percolation temperature and for an additional (magneto)resistivity increase in systems with MPs and other spatially inhomogeneous materials containing FM phase.