We usually use “enroll in” when we use words like course or a program. We use “enroll at” when we name the University or School.
I am enrolled in the Computer Science course.
I am enrolled at Stanford.
You can spell enroll with one “l” or two. Enroll is preferred in American English and enrol in British English.
We use the preposition “in” when we want to show that something exists in a volume or within the boundaries of something. Thank could be “in a park”, “in a field” or “in a bottle”.
Let’s look at some examples of enroll with the preposition “in”:
He enrolled in University last September.
Enrollments in the program must end by Friday the 13th.
In the examples above you use “in” with University because it is a place with a volume. We use “in” with “program” because the program also has boundaries even if they are not physical boundaries.
“Enroll on” is also used because in British English people say “on a course” instead of “in a course” sometimes.
He enrolled on a course last week.
In my experience(I am from Ireland) people do say “on a course” especially for short courses like training. For those courses you tend not to have to enroll” and for that reason “enroll on a course” is not very common.
We use “enroll at” when we mention a specific location like the name of a school or University.
I am enrolled at Oxford University.
Guide to understand why we use in, on and at
We use “at” as a reference point or for a specific location. Think about this. This idea is very important. When you are walking down the street and your friend calls you and he wants to know where you are (your position on the street). You look up and see Mcdonalds and you say “I am at McDonald’s”. McDonald’s is the reference point and your friend knows where McDonald’s is.
We use “in” to show that something is inside a volume. This can be obvious like in the example “the water is in the glass” or not so obvious ”I am in the park”(I am in the boundaries of the park)
We use “on” for surfaces. We want to show that an object is supported by that surface. The book is on the table. The book is supported by the table. We also use this for walls or doors too(or even ceilings). The light is on the ceiling. An important modern example is that everything on a screen we use on.