As an author, you need to ensure that any copyright agreements with journal publishers include permission to submit to PubMed Central.
Either the publisher will ask if the article is NIH funded and will submit for you.
They will allow you to submit the article to PubMed Central via the NIH Manuscript Submission system.
NIH has provided 4 Submission Methods for articles that fall under the Public Access Policy. Check your Copyright Agreement to find out what your publisher will do for you.
Method A: If your article is published by one of the journals that submit all articles to PubMed Central (PMC) on behalf of its authors, you will not have to submit the article yourself. Note that some journals deposit all articles into PMC but they are on a time delay that will not comply with the Policy.
Method B: If your article will be published in another journal you can ask to have the final published article submitted on your behalf. You might have the option of paying for Open Access. Some publishers will submit an article to PMC for you as part of your paid package. NIH has provided a list of publishers who have this arrangement. Note: You can include Open Access fees in your grant application.
Method C: You may also submit your article directly to PMC using the NIH Manuscript Submission system. The NIHMS Help page includes FAQs and useful tutorials on the submission process.
Method D: Certain publishers will deposit the final peer-reviewed manuscript but the author is responsible for approving the paper for processing and display.
NOTE: Methods C & D require the author to approve PDF and web versions of the articles via emails sent from the NIHMS. You may need to check your Junk Mailbox for these emails.
Once you have checked copyright and how your article will be submitted to PubMed Central, you need to make sure your citations are in My Bibliography in My NCBI and mark them with their compliance status and funding information.