Reading and annotating research papers on iPad
How to read, highlight and handwrite on research papers on an iPad, keep everything in sync with your computer, and turn annotations into notes, with ScholarThread and the other apps researchers use.
Short answer: pick an app that keeps your papers in sync with your computer, lets you write with Apple Pencil without your palm leaving marks, and lets you get your annotations out again. ScholarThread's iPhone and iPad app does that for a whole research library: PDFs and EPUBs, highlights with notes, handwriting that syncs, and notes that link back to the passage, all shared with the web app on your computer.
What matters for papers on an iPad
- Your library is already there. You should not have to email PDFs to yourself.
- A pen that behaves. Apple Pencil draws; your fingers scroll and zoom.
- Annotations that sync, so a note made on the sofa is on your laptop when you write.
- Notes that point back to the source, so a quote in your draft can be checked in one tap.
- Offline reading, for trains, planes and library basements.
- A way out, so your notes are not locked in one app.
ScholarThread on iPad
ScholarThread is one app for iPhone and iPad, on the App Store.
- Your library, including Zotero. Papers you add on the web, or import from Zotero, are in the app when you sign in.
- PDFs and EPUBs in one reader, with a table of contents, a list of your annotations and page thumbnails. It remembers where you stopped, across devices.
- Highlights in five colours, each with an optional note.
- Handwriting with Apple Pencil, using Apple's own pens, eraser and lasso. Only the Pencil draws, so you can rest your hand on the screen. Ink stays pinned to its place on the page at every zoom level. See writing on PDFs with Apple Pencil.
- Works offline. Once a PDF is downloaded you can read it and write on it without a connection, and your handwriting syncs when you are back online.
- Sync everywhere. Highlights and notes appear on your other devices and in the web reader, where your handwriting is shown read-only.
- Notes that link back. Literature and concept notes link to papers and passages, and export as plain Markdown to Obsidian or Git.
- Search by meaning on the device, without sending your library to a server for that search.
Other apps researchers use
| If you mainly want to | Consider |
|---|---|
| Annotate the PDFs in your Zotero library and keep using Zotero for everything else | Zotero's own iPhone and iPad app |
| Pull excerpts from several documents onto a canvas and link them | LiquidText |
| Turn annotations into mind maps | MarginNote |
| Handwrite in notebooks and mark up the odd PDF | GoodNotes or Notability |
| Edit and sign PDFs in general | PDF Expert |
| Read, highlight, handwrite and take linked notes across a whole research library, in sync with the web | ScholarThread |
Checked on 27 October 2026. Each app's own site has its current features and prices.
A simple setup
- Keep your references where they are, in Zotero or added directly. See ScholarThread for Zotero users.
- Read on the iPad: highlight what matters, and write in the margins with the Pencil.
- When a highlight is worth keeping, give it a note, or start a literature note for the paper.
- Back at your computer, your highlights and notes are already there. Link notes into concepts and claims, and write from them.
The literature-review note-taking workflow goes through this step by step.
Limits worth knowing
- Handwriting works on PDFs only. EPUBs reflow their text, so there is no fixed page to write on.
- Handwriting shows in scrolling view; page-flip mode does not show it yet.
- On the web you can see your handwriting but not add to it.
- The Android app is in development and does not support handwriting yet.
- Handwriting is not recognised as text, and the AI features never read it.
If something here is out of date or wrong, tell us.