The first objective of this study was to demonstrate the usefulness of the microencapsulation technique to protect fumaric acid and thymol, avoiding their early absorption and ensuring their slow release throughout the gastrointestinal tract (GIT). For this purpose, the release of a lipid matrix microencapsulated brilliant blue (BB) was assessed in vitro, using a simulated broiler intestinal fluid, and in vivo. In vitro results showed that more than 60% of BB color reached the lower intestine, including 26.6 and 29.7% in the jejunum and ileum, respectively. The second objective was to determine the effects of microencapsulated fumaric acid, thymol, and their mixture on the performance and gut health of broilers challenged with a short-term fasting period (FP). One-day-old male ROSS 308 chickens (n = 280) were randomly distributed into seven treatments, with 10 replicates of four birds each. Dietary treatments consisted of a basal diet as negative control (NC), which was then supplemented by either non-microencapsulated fumaric acid (0.9 g/kg), thymol (0.6 g/kg), or a mixture of them. The same additive doses were also administered in a microencapsulated form (1.5 and 3 g/kg for the fumaric acid and thymol, respectively). At day 21, chickens were subjected to a 16.5-h short-term FP to induce an increase in intestinal permeability. Growth performance was assessed weekly. At day 35, ileal tissue and cecal content were collected from one bird per replicate to analyze intestinal histomorphology and microbiota, respectively. No treatment effect was observed on growth performance from day 1 to 21 (p > 0.05). Microencapsulated fumaric acid, thymol, or their mixture improved the overall FCR (feed conversion ratio) and increased ileal villi height-to-crypt depth ratio (VH:CD) (p < 0.001) on day 35 of the experiment. The microencapsulated mixture of fumaric acid and thymol increased cecal abundance of Bacteroidetes, Bacillaceae, and Rikenellaceae, while decreasing that of Pseudomonadaceae. These results indicate that the microencapsulation technique used in the current study can be useful to protect fumaric acid and thymol, avoiding early absorption, ensure their slow release throughout the GIT, and improve their effects on fasted broiler chickens.