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Topological quantum computation (TQC) is one of the most striking architectures that can realize fault-tolerant quantum computers. In TQC, the logical space and the quantum gates are topologically protected, i.e., robust against local disturbances. The topological protection, however, requires rather complicated lattice models and hard-to-manipulate dynamics; even the simplest system that can realize universal TQC--the Fibonacci anyon system--lacks a physical realization, let alone braiding the non-Abelian anyons. Here, we propose a disk model that can realize the Fibonacci anyon system, and construct the topologically protected logical spaces with the Fibonacci anyons. Via braiding the Fibonacci anyons, we can implement universal quantum gates on the logical space. Our proposal is platform-independent. As a demonstration, we implement a topological Hadamard gate on a logical qubit through a sequence of $15$ braiding operations of three Fibonacci anyons with merely $2$ nuclear spin qubits. The gate fidelity reaches 97.18% by randomized benchmarking. We further prove by experiment that the logical space and Hadamard gate are topologically protected: local disturbances due to thermal fluctuations result in a global phase only. Our work is a proof of principle of TQC and paves the way towards fault-tolerant quantum computation.