The electrodes shown at the right would be in the vacuum chamber, which is flat, in a narrow gap between the two poles of a large magnet.

In the cyclotron, a high-frequency alternating voltage applied across the "D" electrodes (also called "dees") alternately attracts and repels charged particles. The particles, injected near the center of the magnetic field, accelerate only when passing through the gap between the electrodes. The perpendicular magnetic field (passing vertically through the "D" electrodes), combined with the increasing energy of the particles forces the particles to travel in a spiral path.

With no change in energy the charged particles in a magnetic field will follow a circular path. In the Cyclotron, energy is applied to the particles as they cross the gap between the dees and so they are accelerated (at the typical sub-relativistic speeds used) and will increase in mass as they approach the speed of light. Either of these effects (increased velocity or increased mass) will increase the radius of the circle and so the path will be a spiral.

(The particles move in a spiral, because a current of electrons or ions, flowing perpendicular to a magnetic field, experiences a perpendicular force. The charged particles move freely in a vacuum, so the particles follow a spiral path.)

The radius will increase until the particles hit a target at the perimeter of the vacuum chamber. Various materials may be used for the target, and the collisions will create secondary particles which may be guided outside of the cyclotron and into instruments for analysis. The results will enable the calculation of various properties, such as the mean spacing between atoms and the creation of various collision products. Subsequent chemical and particle analysis of the target material may give insight into nuclear transmutation of the elements used in the target.

For several decades, cyclotrons were the best source of high-energy beams for nuclear physics experiments; several cyclotrons are still in use for this type of research.

Cyclotrons can be used to treat cancer. Ion beams from cyclotrons can be used, as in proton therapy, to penetrate the body and kill tumors by radiation damage, while minimizing damage to healthy tissue along their path.

Cyclotron beams can be used to bombard other atoms to produce short-lived positron-emitting isotopes suitable for PET imaging.

The cyclotron was an improvement over the linear accelerators that were available when it was invented. A linear accelerator (also called a linac) accelerates particles in a straight line through an evacuated tube (or series of such tubes placed end to end). A set of electrodes shaped like flat donuts are arranged inside the length of the tube(s). These are driven by high-power radio waves that continuously switch between positive and negative voltage, causing particles traveling along the center of the tube to accelerate. In the 1920's, it was not possible to get high frequency radio waves at high power, so either the accelerating electrodes had to be far apart to accommodate the low frequency or more stages were required to compensate for the low power at each stage. Either way, higher-energy particles required longer accelerators than scientists could afford.

Modern linacs use high power Klystrons and other devices able to impart much more power at higher frequencies. But before these devices existed, cyclotrons were cheaper than linacs.

Cyclotrons accelerate particles in a spiral path. Therefore, a compact accelerator can contain much more distance than a linear accelerator, with more opportunities to accelerate the particles.

The spiral path of the cyclotron beam can only "synch up" with klystron-type (constant frequency) voltage sources if the accelerated particles are approximately obeying Newton's Laws of Motion. If the particles become fast enough that relativistic effects become important, the beam gets out of phase with the oscillating electric field, and cannot receive any additional acceleration. The cyclotron is therefore only capable of accelerating particles up to a few percent of the speed of light. To accommodate increased mass the magnetic field may be modified by appropriately shaping the pole pieces as in the isochronous cyclotrons, operating in a pulsed mode and changing the frequency applied to the dees as in the synchrocyclotrons, either of which is limited by the diminishing cost effectiveness of making larger machines. Cost limitations have been overcome by employing the more complex synchrotron or linear accelerator, both of which have the advantage of scalability, offering more power within an improved cost structure as the machines are made larger.