Something secondary is second most important. This can also refer to things that are not important at all.
If you have a primary duty, that's what you need to do first. Secondary duties must be done next, since second is a form of the number two. You could say your secondary goal at a job is to get experience, if your main goal is to make money. Also, people will sometimes say, "This is our goal. Everything else is secondary." That means other concerns are trivial or unimportant. Either way, secondary things never come first.