Think about what kind of Science Fiction short story you want to write. Science Fiction is an extremely diverse genre. Some science fiction stories address issues of technology and its implications for society. Other stories use fantastic worlds as a way to explore complex social issues. Other Sci-Fi stories have a horror emphasis, while others deal with militaristic futures and space battles. Take some notes about what you want to write.
Sketch out the bare bones of your story. Use the following questions to get you started:
Who is your protagonist?
What does he want?
What happens to him?
What does his world look like?
What background information does the reader need to know for this story to make sense?
About how long should this story be?
Write the first draft of your Science Fiction short story. In the unlikely scenario that it comes out as a gorgeous, finely crafted work of art, congratulations! If it comes out the first time as little more than a description of events, that's fine too.
Go back and look at your story. Does it make sense to someone who knows nothing about the world and the character but what you have told them? Add any necessary details.
Reread your story again. Does it pull you in, or just blandly explain things to the reader? Rewrite it, following the rule "show, don't tell" for example, instead of saying "the captain was very stressed out and nervous because he did not know if the space ship had enough fuel for the return flight to Lemuria," you could say "the captain looked at the fuel gauge and felt beads of cold sweat form on his forehead, as a queasy rumbling churned the pit of his stomach."
Edit your story one last time. This time edit for spelling, grammar and word choice. Take out any redundant passages or unnecessary details that don't add to the story.