Boil the pomegranate juice, sugar, and lemon juice in a saucepan over medium-high heat. When the juice boils, reduce the heat to a medium-low. You should see the liquid boiling very gently in the middle.
Let the mixture simmer for about an hour, uncovered. Stir occasionally to make sure that the sugars don't stick to the bottom of the saucepan.
After 45 minutes of simmering, you'll notice that a lot of liquid has burned off. Reduce the heat very slightly and let it simmer for another 15 minutes or so. Take a spoon and dip it into the molasses. If it coats the spoon, the molasses is done cooking (see photo in blog post for a visual).
Turn off the heat and let it cool for 30 minutes before pouring it into a jar. The mixture will still be runny, but don't worry. The molasses thickens as it cools.
This recipe should yield about 1 cup and 2 tablespoons of pomegranate molasses. Store the molasses in the refrigerator for up to 6 months.