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Are you referring to Facebook pixel conversion tracking?
I checked the FB help page on how to use the "Retargeting Pixel"https://www.facebook.com/business/a/online-sales/custom-audiences-website
As per there requirement the code should be pasted with in the <head> ... </head>" tags. This is what their guide says:
Place the pixel code provided by Facebook across your web pages. To do this, copy 100% of the pixel code from the Create Web Remarketing Pixel box, and paste it between the <head> and </head> tags on all pages of your website. Or, send the pixel code to your website developer.
I believe you can achieve your requirement by creating your own custom page and add the "Retargeting Pixel" code within the <head> tag of your page. You can then use this page in our custom thank you URL. The following guide should help you:
Unfortunately it is not possible to add Pixel Code on the original JotForm Form in the Header Tab. You would need to add the script to your website to make it work.
Hope this helps. Let us know if you need further assistance.