Tonight will be my 4 ( out of 5 ) nights using the metronidazole gel. How long does it typically take for bacterial vaginosis to go away while using the gel? I have a lot of burning when I pee today and it doesn’t seem like things are getting better. Does it take even longer after your done with the medication to get better? I originally was supposed to take the metronidazole orally, but I am 8 weeks pregnant and having awful all day sickness and was afraid it would make me even sicker, so they prescribed the gel for me.