In a nonreactive medium saucepan, combine the vinegar, sugar, salt, mustard seeds, cloves and peppercorns. Cook over medium heat, stirring occasionally, until the sugar is just dissolved, about 5 minutes. Add the ginger, then use a vegetable peeler to slice strips of zest from the lemon; add to the saucepan. Let the liquid cool to room temperature, about 30 minutes.
Divide the rhubarb among 3 clean, small glass jars. ladle in the cooled brine mixture. Top with the lids and refrigerate the pickles for 2 days before eating. (The pickles will keep refrigerated for up to 1 month.)