Trapped ions are excellent candidates for quantum computing and quantum networks because of their long coherence times, ability to generate entangled photons as well as high fidelity single- and two-qubit gates. To scale up trapped ion quantum computing, we need a Bell-state analyzer on a reconfigurable platform that can herald high fidelity entanglement between ions. In this work, we design a photonic Bell-state analyzer on a reconfigurable thin film lithium niobate platform for polarization-encoded qubits. We optimize the device to achieve high fidelity entanglement between two trapped ions and find >99% fidelity. The proposed device can scale up trapped ion quantum computing as well as other optically active spin qubits, such as color centers in diamond, quantum dots, and rare-earth ions.