Yes, probably.
An academic CV should be a comprehensive record of your academic past. It is not like a professional resume where you include precisely the (true!) information that you think will be to your advantage. It is very likely that anyone reading your CV will assume that they are looking at the complete list of your publications. So omitting a paper because you think it will make the reader think worse of you is something that, if discovered, would be regarded as inappropriate by many. (And in many academic fields nowadays, such a discovery would be quite easy to make.) If it is a standard convention in your field to include only "selected publications" in your CV, you could do that...but of course it could make the reader curious as to what was not selected.
Let me also say that not wanting to include a publication because of the low impact factor of the journal it was published in is at least one step further along on the path to impact factor insanity than I had heretofore heard of. A paper is not good or bad because of some numerical measure of the journal it is published in. Further, not all papers are our best papers and this is so obvious that there should be no shame in it. However, if you really think that a paper is so weak that you might later regret publishing it: think harder, and if you're convinced then don't publish it.
Added: According to @ff524's comment, the impact factor may be the least of your worries. But I think my answer applies even if you're published in a "predatory" journal.
Further Added: People may be interested to know that I have a publication in a journal whose publishing company, SCIRP, is on Beall's list. I won't tell the full story of how I came to publish the paper there except to say that this is a journal in which one ostensibly has to pay to publish, I was curious what happens when one submits to this journal and is not willing to pay, and in the answer in my case is that they published the paper anyway. (Yes, this "experiment" was not well thought out nor necessarily ethical behavior on my part.) Moreover, my opinion of the journal has declined in the intervening years since I published the paper. Nevertheless I list the paper on my webpage and on my CV: on the one hand, I feel obligated to. On the other hand, despite the fact that the paper was published in a journal some of whose practices look pretty shady, the paper itself is a real (though rather modest) research contribution. In fact, from what I can tell (the subject of specialty of the journal lies outside of my core expertise) a good number of the papers published in this journal are solid. (So the journal is in some ways predatory and some ways legitimate. I find this very strange, wish I understood the situation better, and again, I wish I hadn't published there.) I would much rather have a line on my CV that shows that I made a naive, questionable choice of where to submit a paper than have a CV which is not intellectually honest.
Yet Further Added: I will record here what I found on the web concerning the question of whether an academic CV should list all publications.
1) This link from UC Berkeley's Guide to CV's as part of an academic job search says "List all the papers and presentations you have delivered or will deliver."
2) Our trusted friends at Elsevier weigh in on the subject and seem to come to the opposite conclusion:
It is advisable to list your most reputed publications in ranking of type, such as books, book chapters, peer-reviewed journal articles, non-peer-reviewed articles, articles presented as prestigious conferences, forthcoming publications, reports, patents, and so forth. Consider making an exhaustive list of all publications in an appendix.
Please direct further questions on this article to its author, "Elsevier Biggerbrains."
3) Caroline Eisner at academic coaching and writing says
When you list your publications, begin with the most recently published, or those out for review (list these in italics), and move down your list to the one published first. If there are early publications (or conferences) you are no longer proud to list, or you no longer care to publicize, leave them off the list. If you delivered a paper long ago, and it is not relevant to your current academic self, don’t include it.
4) This University of Washington guide to academic CVs writes
List your published works in reverse chronological order according to publication
date. Use the reference style appropriate to your discipline. If you have multiple publications,
consider dividing them by type such as articles and book chapters, or
refereed and invited
papers. If an article has been accepted for publication, indicate ‘in press’ or ‘forthcoming’ in
lieu of the publication year. Consider bolding your name on each publication.
It seems to give the impression that all publications should be listed. (There is also the implication that there will not be so many.)
5) The University of Kent counsels structuring the CV so that the most relevant publications are highlighted, but the implication is that all should be included.
