"pick you up" is the only correct one of the two you listed.
Getting into more details though, note that this is a pattern involving a verb and an adverb, which has a dual form.
1. I'll pick you up - [Verb + PRONOUN + Adverb] if the object is a pronoun.
2. I'll pick up my friend - [Verb + Adverb + NOUN] if the object is a regular noun (phrase).
So we say "I botched it up" and never "I botched up it", for example.
But also note that there are similar looking phrases with a preposition, for which we must put it before the noun or pronoun.
For example,
- I rely on you - "on" here is a preposition, so it cannot come after "you".
"up" and "on" can be both an adverb and a preposition, so it is not always obvious which capacity they are being used in. You need to have a good understanding of their general usages, as well as how they combine with certain verbs.
For example, here are more complex cases.
- He took off his jacket - is "off" an adverb or a preposition?
- He took his jacket off - "off" is an adverb, so it can come before or after a noun.
- He took it off - but not before a pronoun.
(We know "off" is an adverb because it describes the whole action ("separating"), not limited to the "jacket")
- I'm going to beat him up - adverb. ("up" describes thoroughness of the action)
- I walked up the grade - preposition. ("up" describes how the action relates to the grade primarily)
- The children look up to their teacher - "up" is an adverb, "to" preposition (some people consider "up to" as a compound preposition).