This answer relates to EndNote 21, and is adapted from the instructions prepared by Federation University Library: https://libguides.federation.edu.au/c.php?g=831677&p=6199335
1. In EndNote Desktop, ensure Vancouver style is selected by clicking Tools > Output Styles > Vancouver
2. Then click Tools > Output Styles > Edit "Vancouver"
3. In the Citations section of the Vancouver style editor, click Templates​
4. Delete the parentheses (round brackets) from both the displayed templates. Select each instance of Bibliography Number and set it to superscript by clicking the option highlighted in the screenshot below. Do not make the text for Author into Superscript
5. Close the style editor by clicking the corner X and, when EndNote asks about saving changes to Vancouver style before closing, click Yes
7. When it asks you to rename the modified style. rename it to something meaningful e.g. Vancouver (superscript)
8. To use this new superscript style in EndNote, click Tools > Output Styles > Open Style Manager
9. Tick your modified Vancouver style in the list of available styles and close the Style Manager
10. Your modified Vancouver style will now appear in the list of available styles in EndNote and Cite While You Write, enabling you to create superscript in-text numerical citations in Word