The aim of this study was to examine whether and to what extent the supplementation of feed with a coated or non-coated mixture of fatty acids (caprylic and capric acid) affects broiler chickens experimentally infected with Campylobacter jejuni. The study was carried out using 48 chickens divided into four experimental groups. Throughout the whole rearing period (1–42 days), the chickens were fed a diet supplemented with 0.25% caprylic and capric acid (1:1), coated or non-coated. At the age of 14 and 28 days, chickens were orally challenged with C. jejuni. At regular time intervals post-inoculation, the shedding of C. jejuni was assayed using quantitative real-time PCR. Both supplements significantly decreased faecal C. jejuni counts by 1.2–4.1 log10 CFU/g 4 days post-inoculation; after this time period, the effect of medium-chain fatty acids (MCFA) was less pronounced or absent. Campylobacter jejuni counts in excreta samples were significantly lower in chickens fed coated MCFA than in those fed non-coated MCFA. No effect of MCFA on feed intake or growth of chickens was observed. In conclusion, (i) MCFA are active against C. jejuni and (ii) the encapsulation enhanced the efficacy of the acids. These results allow the recommendation of using MCFA as feed additives in chickens, preferably 2–3 days before slaughter.