Fill out a character profile. Find sample questions online, or create your own. Include your protagonist's physical appearance, background, likes and dislikes, personality traits, habits and quirks. Get to know your character before writing the story.
Create a second character profile for your protagonist. Include the same questions, but this time answer them as if your character has already experienced the events in your story. Ask yourself how the story will change your character, and include those changes in the new character profile. This second profile will help you keep the end goal for your protagonist in mind.
Give your character flaws. Nobody is perfect, and a perfect protagonist won't ring true to your readers. Create a character they can relate to. Give your character quirks, bad habits, fears or emotional weaknesses that must be overcome throughout the story. Try creating an anti-hero, a protagonist that seems more like a bad guy than a hero.
Write about half of your story. Pause to evaluate your protagonist. Ask yourself where he is at this point of the story, and if he is developing the way he needs to in order to defeat the antagonist at the end. If he is stagnant, revisit what you have written and try to include some elements of change. Stagnant protagonists can be boring to readers. Create a third character profile, describing your protagonist at this stage, if you feel it will help you evaluate his growth.
Allow your protagonist to make her own decisions. Don't try to stuff her into the events of the story. Take her personality and past into consideration. They will affect the way your character thinks and acts. These actions will in turn affect the development of your story, and your protagonist, and make them more believable. For example, a character who once had a broken heart, and now distrusts men won't jump right into a romantic relationship. Instead of a whirlwind romance, a connection might build slowly throughout the story.