In the late 1940s, Henry Torrey at Rutgers University and, independently, Erwin Hahn at the University of Illinois took a new step forward in NMR by applying pulses of strong radio waves to the sample instead of a single continuous wave. They first observed transient NMR signals during the application of long pulses. Following Hahn's later observations that transient NMR signals could be measured after the application of short pulses, the pulse technique became an important method for physicists and chemists investigating atoms and molecules.

Additionally, Hahn discovered a phenomenon known as "spin echo," which proved important for measuring relaxation times. At first he attributed these seemingly spurious signals to a misfiring of his electronics. After more study he recognized that they were caused by the speeding up and slowing down of the spinning nuclei due to variations in the local magnetic fields. By applying two or three short radio pulses and then listening for the echoes, Hahn found that he could obtain even more detailed information about nuclear spin relaxation than he could with a single pulse.

Pulsed NMR and spin echoes would play a crucial role in the development of magnetic resonance imaging two decades later. At the time, however, the idea of using NMR to make images simply did not occur to scientists using NMR spectra in physics and chemistry. In any event, before NMR could become a practical imaging tool, some further steps were needed. One important aid was a new pulse method called Fourier transform NMR, first proposed by Russell Varian of Varian Associates in the late 1950s. At about the same time, Richard E. Norberg and Irving Lowe at Washington University in St. Louis showed experimentally and theoretically how one could get all the results available from continuous wave experiments by mathematical manipulation of the signals produced in a pulse experiment. However, at that time the mathematical step needed to analyze the pulse data (a technique called Fourier transformation) was impractical because of the limitations of the computers available.

In the late 1960s, Richard Ernst and Weston Anderson, while working at Varian Associates, were studying the complex many-line NMR spectra of interest to chemists. It was a slow process searching by trial and error for the frequencies to produce all the many lines of the spectra. They realized that simultaneously broadcasting a range of radio frequencies at the atoms in the sample and then performing Fourier analysis of the resulting pulse signal could give all the results of the continuous wave method. This technique was thousands of times faster than the old method, and it also allowed researchers to observe signals only one-tenth as strong. By then advances in computers had made Fourier transformation practical. It now became possible to use NMR to analyze very small samples of a material or to identify very rare atoms in larger samples. In 1991, Ernst won the Nobel Prize in chemistry for his contributions to the development of high-resolution NMR spectroscopy.