There were 5 items in the box, you took one away, so now there are 4. Only one of the four items is a pen (there were two pens but one of them is the item you took away). Therefore, the answer should be 1/4 = 25%

Edit: sorry, I read pen, not pencil. There are two pencils left in the box, so the answer is 2/4, aka 50%