First, list the items you absolutely need in your bathroom. This list includes, of course, the toilet and the sink. If it's a full bathroom, you'll need to decide on a bath and shower or a shower stall.
Next are the items you would like to include. Often people want a cabinet under the sink, though if you have a small space you might prefer a pedestal. Plan on a mirror over the sink, with our without a medicine chest. Lighting is important. A fan can be helpful for keeping moisure out. You'll probably want a space for shelves of some kind.
At this point, you might want to consider asking a professional to help with design. If you feel you can do it on your own, here are some tips.
Measure your bathroom well. Choose items that you think you'd like in your bathroom and get the measurements. Some suggest drawing a plan to scale, but for those of us who are less visual, it can be helpful to cut paper to the actual size of the footprint of the item. Place these items in the bathroom, arranging them to where you think you would like them. This is a good way to see how well things fit. Don't forget that you need space between things.
If everything fits well, there are a few more considerations. You might be limited by plumbing or electricity. Window placement makes a difference, too, unless you have no qualms about showering in from of a window.
If things don't fit well, play with the design a bit (if space, electrical, and plumbing allow.) See if you can come up with more efficient use of space and still enjoy the design.
If there's just no room, you'll have to decide what you can do without. For example, you can use a pedestal sink, which takes less space than a full cabinet. Conversely, you can use a cabinet but don't include shelves. Some towels and toilet paper can be stored in the cabinet, with the excess supplies in a convenient storage area elsewhere in your house.
A little imagination and a lot of measuring can help your dream bathroom work for you. When you find a bathroom design that works, it's time to put the pieces together. It's a lot of work, but it can be worth it.