The NIH has a number of resources further explaining their policy and processes:
The NIH Public Access Policy Journal List comprises those journal titles that deposit the final, published versions of all NIH-funded articles in accordance with the NIH Public Access Policy. Note that these journals may have embargos that hold articles from viewing in PMC for up to 1 year, as allowable by the Policy. These are the Submission Method A journals. The start date of Policy compliance for each journal may vary.
Some publishers will submit the final published article in PMC for the author upon request (and usually for a fee). These are Submission Method B Publishers.
Some publishers will deposit the final peer-reviewed manuscript (not including journal formatting) into the NIHMS system; these require the author to complete all of the remaining steps of the submission process. These are Submission Method D Publishers.
Some publishers require the author to handle the entire process. With these, the author must make certain they include the right to submit the peer-reviewed manuscript or final published article (journals may vary on which form is allowable) to PubMed Central via NIHMS. These are Submission Method C Publishers. It is better to negotiate the submission agreement in advance of publication rather than attempt to correct it post-publication with these journals.
The PMC Journal List offers a searchable list of all the journal titles that have deposited or are currently depositing some of their final, published articles into the PMC archive; the articles submitted may or may not meet Public Access Policy requirements. The journal has independently chosen to submit to PMC regardless of the Policy and the selection of deposited articles may be limited.
See the Manuscript Submission section of this guide for more information on the Submission Methods and how to use the NIH Manuscript Submission System (NIHMS).
Journal Publishers vary widely in their level of compliance. If you know that you must meet the NIH Public Access Policy for your publication, it is highly recommended that you investigate the specific policy of an individual journal before submitting your manuscript to it. Below are some sources of information on journal policies, but note that these may not be complete or current. Always check with the journal itself regarding its present policy.
Always check your copyright agreement before signing! Journal policies can change over time!