Well, I would agree with people commenting about Pickle and Pyxel I hope that's right, I use them from time to time but they tend to be a little buggy and crash on me, however they are a good place to start.
I would like to offer a more efficient workflow though! I would recommend Paint.net and Graphics Gale. Both of which are FREE!
I say Paint.net as it faster and better for working with still or static pixel art, like tiles and other such level assets. Where as Graphics Gale would be your go to for the animation of characters which offers a real time preview of the animations. Although there is another application you could use which is also completely FREE, I believe it's called AeSpriter.
Here, I wrote a tutorial a while back and haven't had too much time to finish off the second part to it but it covers the different applications you could use for pixel art, or at least the most popular ones.https://www.scirra.com/tutorials/582/creating-isometric-pixel-art-from-scratch-part-1-creating-templates/page-3
It will give you links as well as a rough idea for the application too... I hope this helps shed some light on where you may begin =]