Time-bin encoding of photonic qubits is particularly well suited for implementing quantum operations in integrated photonic circuits and fiber-based quantum networks. However, key experimental difficulties are to maintain the phase between time-bins for hours and to perform arbitrary basis transformations. Typically, unbalanced Mach–Zehnder interferometers (uMZIs) are employed, but in fiber-based implementations, their continuous hour-long phase stabilization and rapid change of setpoints for feed-forward operations are challenging. We address these issues by implementing a novel active, low-noise phase stabilization method that utilizes reference pulses and dither locking. To demonstrate the performance of our method, we generated high-fidelity time-bin entangled states at 1560nm from a type-II periodically poled lithium niobate (PPLN) crystal via spontaneous parametric down-conversion (SPDC) and performed full quantum state verification. While maintaining a mean state fidelity of F = 0.966 ± 0.0045, we were able to lock to arbitrary phase setpoints, maintain continuous active locking for 24 hours, and suppress any crosstalk between reference pulses and the quantum channel. This introduces our system as ideal for fibre-based photonic quantum information processing.