Over the past few decades, the field of molecular electronics has greatly benefited from advances in the fundamental understanding of charge transport mechanisms. Molecular junctions represent a field whose potential is realized through detailed studies of charge transport on the nanoscale. Applications of molecular junctions, such as molecular logic circuits, rely on precise mechanistic information as investigative techniques are refined. Current advances have originated from improvements in a variety of characterization techniques, with noise spectroscopy contributing to key studies of transport phenomena. Noise spectroscopy has shown to be useful for probing latent electronic characteristics in molecular junctions, giving insight beyond standard methods of charge transport study. This review presents an in-depth background on fundamental concepts in electronic noise spectroscopy, covering topics such as flicker, generation-recombination, random telegraph signal, and shot noises. Recent advances in noise spectroscopy techniques and their applications to the study of molecular junctions are discussed, highlighting the impact of this technique in the improvement of molecular junction stability and reliability, the study of interference in charge transport, and the emergence of vibrational excitation phenomena. This review provides a comprehensive understanding of noise analyses in the field of molecular junctions and gives insight for further advances in molecular and nanoscale electronics.