In this post, I focus on the administrative and formal aspects of submitting a paper to an academic journal.
As an example, I use a research topic (sometimes called a special issue) of Frontiers (a large academic open access publisher).
First, navigate to the journal (and maybe research topic) page that you intend to submit to. I am not covering this here, but this is a very important strategic decision, as the fit of your paper to the journal is the most decisive factor for the success of your submission. Once you are on the page, just look for a Submit button.
Frontiers even asks you for the fit to the selected journal/research topic explicitly. But even if the publisher doesn’t do this, it is good practice to remind yourself of the fit (best before actually writing your paper!).
Then upload the actual manuscript:
Supplement information, such as title, abstract and keywords.
Add information about the authors and their contributions:
Provide additional information abou data availability, ethics, conflicts of interest, etc.
If it is an gold open access publication, you likely will also have to deal with some financial stuff (e.g., identifying who is going to pay the invoice).