Vanilla JavaScript refers to using plain Javascript without any additional libraries or frameworks. The term became popular when Eric Wastl created the Vanilla JS site in 2012 as a joke. The site tries to bring attention to the fact that you can use just plain Javascript in many cases.
Learning “vanilla” JavaScript means learning the fundamentals of JavaScript. Frameworks and libraries help abstract and simplify some features of JavaScript which makes writing code faster and easier. But in the long run, it is important to know the fundamentals of JS to be able to learn the use of new frameworks faster and decide if a framework is needed at all.