How is fusion reactor fuel initially accelerated? If, in a nuclear fusion tokamak reactor, you start with neutral fuels, how do you accelerate the atoms fast enough to start the reactor?
Or do all of the particles have to ionized to begin with?
 A: In addition to radio waves, as mentioned in the answer by @peterh, there is also another important mechanism which constitutes one of the main advantages of a tokamak: ohmic heating. Let me try to explain.
In a tokamak, as opposed to a stellarator, you drive a strong current in the plasma which generates part of the confining magnetic field. This current also contributes to heating up the plasma, this is what we call ohmic heating. Note that ohmic heating alone is not sufficient to achieve fusion temperatures, for this we need additional heating mechanism like radio waves.
The current in the plasma is induced according to the transformer idea: the plasma is the secondary winding and a central solenoid acts as primary winding. Ramping up a voltage in the latter, induced the plasma current. Or, to be more precise, it creates a strong electric field. This field then accelerates free electrons, which you always have in a gas. Those free electrons trigger an avalanche process which leads to the formation of a plasma. 
Radio waves are often used to support the breakdown in a tokamak, but are not a requirement. In a stellarator, on the other hand, there is no transformer and radio waves alone are used for a breakdown. 
(Note: I interpreted your question to be about the initial breakdown as you mentioned ''start with neutral fuels''.)
A: With radio waves. Essentially, a tokamak is also a large microwave oven.
