Provided herein are gap detection and compensation schemes for timing alignment systems. In certain embodiments, a timing alignment system includes a detector that generates one or more loop control signals based on comparing a reference clock signal to a feedback clock signal, a loop filter having a loop voltage that is adjusted based on the one or more loop control signals, and a gap detection and compensation circuit that processes the one or more loop control signals to detect a gap in at least one of the reference clock signal or the feedback clock signal. In response to detecting the gap, the gap detection and compensation circuit modifies the one or more loop control signals to provide an adjustment to the loop voltage.