I am presently working temporarily at ABC company and my last day is next Friday, thereafter I can come in and meet with you.
Yes, but you have a comma splice, so it sounds wrong.
It would be far more common to use the following word order:
"I am presently working temporarily at ABC company and my last day is next Friday. I can come in and meet with you thereafter."
But if you want to use 'thereafter', you wouldn't use casual language like "come in" or "my last day." You'd need to make the whole sentence rather formal.
"
My current temporary work at ABC terminates on Friday, 12th November. Thereafter, I am free to meet with you." - This sounds a bit stuffy, but it's just to give you an idea. You'd probably want to consider using "after that" instead of "thereafter" in your original sentence.
PS: You can use fancy words like this deliberately in non-serious writing for humourous effect.
"... Fido emerged from his cat fight with more scratches than he had bargained for, and was thereafter less enthusiastic about tormenting the neighbourhood cats."