Where to stay to see the islands

We had Šibenik on our radar for years and finally got there this past September. It was okay, maybe the anticipation was too high but we didn’t love it as much as Split, or even Zadar.
The ferry doesn’t go from Šibenik to the islands you mention, you would have to go from Split.
Check the times and destinations at croatiaferries.com

how many days/where do you fly out/what month?

We have a total of 16 days on the ground. We are flying out of Dubrovnik, which is where we are going to complete our trip.

Sorry the month will be the first two weeks of September 2025

Okay great--early September is a great time for the islands. Are you going to spend time in Zagreb?
Planning to stop at Plitvice? If not, I'd skip the car and zip straight to Split. Some might enjoy staying in one place and doing day trips, but I would choose at least two of the four islands to stay over on, and do day trips to the others (perhaps while staying in Spit if it was in your plans). See catamaran schedules on the Krilo and Jadrolinija websites.
Sibenik sounds interesting for a peek at the cathedral or an alternate to some other towns for a second or third trip, but I always bypassed it. Split is the access points for the islands you selected, with Korcula roughly halfway to Dubrovnik (so good to stop en route).

Here is a rough itinerary you can adjust to your preferences:
Zagreb 1-2
Plitvice 1
Sibenik stop over?
Split 2-3 (day trip to one or two islands)
island 3
island 3
Dubrovnik 2-3

Not staying in Zagreb but going to Pula/Ravinj and surrounding regions for 4 nights then to do Plitvice Park. Afternoon followed by early a.m. next day

Then down to Split. I guess what I need to research is the ferry schedules in more detail. Split is okay but we prefer to stay Korcula as home base. From there day trips to other islands. Just don’t want to get stranded if ferries only run every so ofter

Check the ferry schedules but try to avoid Jadrolinija line. It is the car ferry so it moves slower and is larger and not as comfortable. Look at the schedules for catamarans such as Krilo.

Early September is still the season so catamarans should be daily.

We love Korčula and visit cousins who live there often. Try and stay inside the old town.
You can check out Guesthouse Jungher which is a true B&B with the owners living there. Full disclosure, they are cousins.

Okay in that case:
Istria 4
Plitvice 1
Sibenik stop over?
Split 1?
island 3
island 3
Dubrovnik 3
That leaves one extra night, so if you are not planning on an overnight in Split, you could add one more island for two nights (the minimum IMO).
I don't think the islands are well spaced or linked by adequate catamaran schedules for easy day trips from one to the other. To me, staying on at least one island is preferable to lots of day trips. Some have more "sights" than others, but even though it has few, Vis was one of my favorites (more of a nature lover). Hvar and Brac are close enough together that they are the easiest to go back and forth from, but even that may not be as simple as you might think. For example, you can go from Bol to Jelsa, but then you have a bus or taxi to Hvar town or Stari Grad. You should definitely plan on Korcula en route from the Split area to the Dubrovnik area, as it is right there on the catamaran line/ferry route (some go to Vela Luka, on opposite end of island, but linked by bus).
Of course, there are also private day trips you can do from one to the other, but I would choose at least one island that you want to explore on its own. Brac has several small towns that are appealing, plus a monastery and the famous beach. Hvar and Korcula are relatively similar in attractions--pretty towns, lavender fields or vineyards
Jadrolinija operates catamarans also, schedules will list if it is a car ferry or a catamaran, but Krilo is all cat.

Hello, I agree with other reviewers who suggest that you stay overnight on the islands instead of hopping from one to another.

I travelled to Croatia at the same time this past September and in terms of islands spent 2 nights on Korcula and 2 nights on Mjlet. I can definitely recommend both of them and it is nice to be able to contrast the two. Mjlet in particular had very little tourists at the beginning of September; it was absolutely idyllic and felt as if we had rented the beautiful island for ourselves.

The ferrys are relatively frequent from Korcula to the mainland and back, if I remember correctly I think that they were running every hour. They are less frequent to some smaller islands such as Mjlet ... check particularly in terms of Vis because it is the most difficult island to access.

While it is tempting to go from one island to another by ferry, do remember that some of the in-between island ferries don't take cars or if they do they are quite slow. In my opinion, having a car is indispensable for discovering the islands.

Best of luck !