No. Rules will run in the order they are listed in most cases, but you cannot depend on this when creating rules.
In some cases it could be useful if the rules ran in order. You would be able to create catch-all rules: first move the pdf files somewhere, then move all the rest somewhere else.
The problem is that if rules should run strictly in order, they would also depend on each other. If we cannot move all the pdf files first, then "the rest" might also contain pdf files, and the logic of the catch-all rule is broken. So File Juggler would have to stop processing all following rules.
If file juggler cannot process a rule for some reason, it will go on with the rest of the rules, and try again later. This can happen if it should take action on a file that is being downloaded or is locked for writing because it's open.
So catch-all rules also require that you actively select the rules that should run in order, so other rules will not be affected by pauses or errors. This is not supported, at least yet.