This work aimed to formulate composite hydrogel particles based on two oppositely charged polymers, sodium alginate, and chitosan, prepared by external ion gelation. The dosage form formulation as a self-emulsifying system (SES) carrier was targeted to deliver the insoluble drug thymol to the GIT distal parts. The impact of several formulation variables (the proportional amount of sodium tripolyphosphate and sodium alginate, a type of chitosan, and the amount of incorporated SES on morphological properties, swelling properties, thymol content, and in vitro dissolution profiles over 6 hours were investigated. The most prolonged thymol release was ensured using a higher ratio of tripolyphosphate to sodium alginate and primarily with a higher incorporated SES amount. However, a deeper study on possible use in treating intestinal inflammations is necessary.