The S Pen is an optional add-on for the Galaxy S21 Ultra. But the move will fuel speculation the firm will phase out its separate Note handset range.
Samsung told the BBC it had yet to make a decision about this.
The company's handset sales have declined more quickly than the wider market. One expert said a streamlined line-up might help address this.
"There's increasing logic for Samsung to converge the Galaxy S and Note platforms, because there's so little differentiation between the two kinds of devices now," said Ben Wood, from the CCS Insight consultancy.
"That would align them with Apple, which also has one big phone launch event a year.
"My concern is that every time Samsung has announced its Note products in the past, it has planted a seed in consumers' minds that the Galaxy S products have become kind of the old ones."
The benefit of having a stylus is that it is easier to write, draw or annotate notes than using a finger. But to work it requires special hardware under the glass of the phone's display to pass power to the stylus and to track its tip.
'Expanded Note experience'
The Android-based Galaxy S21 Ultra has a 6.8in (17.3cm) display, which is only slightly smaller than the top-end 6.9in Note.
In years past, the Note phones were known as "phablets", and their size was the other key distinguishing factor with the S range.
Product manager Mark Notton said "we haven't decided", when asked whether Samsung planned to continue the Note family.
"It does not mean that Samsung is not committed to the Note category, but is expanding the Note experience across device categories," the firm said in a follow-up statement.
"We will actively listen to consumers' feedback and reflect it in our continued product innovation."
The S21 Ultra will start at £1,149 when it goes on sale on 29 January. The S Pen costs an extra £35 on its own, or £85 when bundled with a case that stores it.
That puts it in the ballpark of the Galaxy Note 20 Ultra's £1,179 starting price, which comes with a stylus that slots into its body.