Trapped neutral atoms have become a prominent platform for quantum science, where entanglement fidelity records have been set using highly-excited Rydberg states. However, controlled two-qubit entanglement generation has so far been limited to alkali species, leaving the exploitation of more complex electronic structures as an open frontier that could lead to improved fidelities and fundamentally different applications such as quantum-enhanced optical clocks. Here we demonstrate a novel approach utilizing the two-valence electron structure of individual alkaline-earth Rydberg atoms. We find fidelities for Rydberg state detection, single-atom Rabi operations, and two-atom entanglement surpassing previously published values. Our results pave the way for novel applications, including programmable quantum metrology and hybrid atom-ion systems, and set the stage for alkaline-earth based quantum computing architectures.