Or does the timeline just not allow that given the respective lengths of time it took for Earth to evolve complex life vs the time it took for Mars to lose its atmosphere? Could an alien civilization have flourished on Mars long ago before being wiped out or is there just no chance of that being possible without the aliens being colonists from another star system?
So cut off the Earth timeline at 3500 million years ago. I see that’s where single-celled life was just evolving photosynthesis. Then, everything dries up. Life, if it remains, has to adapt to living underground and does not have access to this high energy source.
Now another planet may be faster or slower, but considering how many steps are still needed, even if the steps that were delayed on Earth are hastened, there’s just not enough time by orders of magnitude.
I also think that Mars would progress slower given the smaller sample and the statistics of things happening.
There is absolutely no scientific answer to your question. There cannot be one.
Future research might change this:
What happened here on Earth has not been correlated to any extraterrestrial biogenesis and development much less sentience and very much less sapience. Without any data, it's all idle speculation.
Taking Earth as a baseline is a reasonable approach to a WAG, but it has no more scientific validity than assuming one of the many unexamined differences had some profound effect on rates.
Upshot: Assuming human development as the required time-line, pretty much, no. Of course, the time it takes for a random event to occur is random.
Can you write a hard sci-fi story with intelligent Martians? Sure.
We can only really make guesses as to how this might work.
The only place we know where life has developed is Earth. In fact, there's still a non-trivial amount of people who don't think even that is true - it might very well be that primitive life came to Earth from elsewhere. So let's assume that primitive life appeared on Mars as soon as it was hospitable to it at all, and let's assume further that it already had the ability to do photosynthesis (this is rather generous, but let's go with this).
Let's try to come up with something that would work in a story. This necessarily means a lot of guesswork and luck :)
Mars is smaller than the Earth. The development of complex organisms on Earth started after the atmosphere got a big chunk of oxygen, which in turn required all the iron dissolved in the ocean to be precipitated as iron oxides - iron simply reacts with oxygen too readily to allow much free oxygen in the atmosphere. On Earth, this took a billion years - we need to make this a lot faster. So, make sure you have a lot of shallow shelf seas and more volcanic activity than Earth, and you can easily cut this to just maybe a hundred million years (of course, we don't know how much water Mars had four billion years in the past, so you can give yourself some wiggle room). Now you have oxygen-breathers, which quickly grow in complexity (thanks to the metabolic boost from oxygen, and the damaging effects of free oxygen radicals).
There's plenty of oxygen in the atmosphere to form ozone - and with it, protection against UV radiation from the Sun. This makes land life possible - but on Earth, this actually took another two billion years, leaping through stages like multi-cellular life and sexual reproduction. Why? Well, we're not really sure, but for story purposes, let's assume that this was mostly because there wasn't much of an area for life to live at that point - most of the Earth was either the deadly land, or oceans too deep for life. In your Mars, the lower amount of water and smaller size of the planet meant that there was much more shelf seas, ideal for life. You still need some continental movement (and unlike Earth, there would be a lot of land, even though not quite the same kind), but assuming Mars had the same amount of radioactives per mass, it would be a lot more active (the usual square-cube ratio).
The development of life seems vaguely logarithmic, especially since sexual reproduction, so we can guess that doubling the amount of liveable space (while still including periods of isolation and reunion) might make the progress much faster than on Earth. We'd only need about five times faster, which isn't too implausible given the right conditions.
So, 3.5 Gyr ago, Mars was hosting a living civilisation. They flourished, explored the solar system even, but they ultimately managed to die out. The trickiest point in your story is that it's extremely unlikely anything of their civilisation would survive for 3.5 billion years. Mars was still geologically active for another billion years or so, and the life that survived the Martians would quickly destroy ("recycle") most of the remnants. The rest would be swiped through erosion, oxidation etc. Maybe, as a huge stretch, a well isolated place deep inside an ancient continent might have something worthwhile - something like a golden tablet with inscriptions. But don't expect to find any technology, any things of daily life - those would have long since turned into dust.
There's few places where you could expect anything to survive for this long. A monument on the Moon, with a golden plaque (or the Encyclopaedia Martinica :)) hidden deep enough underground, that managed to avoid all impacts (quite a tall order!)... maybe. Something the Earthlings found during excavations of the first Lunar colony? But don't expect to find anything else - certainly not the kind of archeology we do on Earth. Even if they designed it to last forever, almost everything would be gone in a few billion years.