The short answer is no, Multisite uses the domain name to determine which site you are on, so there is no way to set up a Multisite site in a subfolder.
Having said that, depending on what you want to achieve there’s often ways around it.
For example, if you were ok with using a separate WordPress installation for the subfolder site, you could create the subfolder manually, set up WordPress in it, and there you have it – alongside your main Multisite install in the root. Of course, this could get messy if you have a lot of these subsites, and again, it really depends on your goals.
In the end, anything is possible with enough time and resources, but from the information you’ve provided so far it sounds like it’s not easily possible with the default way Multisite works.