A magnetic skyrmion induced on a ferromagnetic topological insulator (TI) is a real-space manifestation of the chiral spin texture in the momentum space, and can be a carrier for information processing by manipulating it in tailored structures. Here, we fabricate a sandwich structure containing two layers of a self-assembled ferromagnetic septuple-layer TI, Mn(Bi$_{1-x}$Sb$_{x}$)$_{2}$Te$_{4}$ (MnBST), separated by quintuple layers of TI, (Bi$_{1-x}$Sb$_{x}$)$_{2}$Te$_{3}$ (BST), and observe skyrmions through the topological Hall effect in an intrinsic magnetic topological insulator for the first time. The thickness of BST spacer layer is crucial in controlling the coupling between the gapped topological surface states in the two MnBST layers to stabilize the skyrmion formation. The homogeneous, highly-ordered arrangement of the Mn atoms in the septuple-layer MnBST leads to a strong exchange interaction therein, which makes the skyrmions soft magnetic. This would open an avenue towards a topologically robust rewritable magnetic memory.