I ask this because in an exercise in my book it says to use をする with 電話 to form the verb, but on the online dictionary I usually check it says it's 電話する, without を.
Similar to fefe's answer on a closely related question, 電話をする is really a phrase, not a "word", so it probably wouldn't show up in a dictionary as a unit.
In this case, it might be fair to say that the meanings are the same. In some ways it can be compared to "I'll give X a call" vs "I'll call X". There are corner cases where the former could sound "odd", but for all practical purposes they mean the same thing.
One technical note: を shouldn't be used with 電話をする to indicate the topic of the phone call, whereas it can be used with 電話する... following a more general rule about not having more than one を in a clause.