Treatment of Canine Urinary Tract Infection. Antibiotics are used to treat the bacterial infection for a period of 10 to 14 days. There are different types of antibiotics that are selected based on the sensitivity of the bacteria and the extent of the problem. Your dog should start to feel better within 48 hours. These are highly effective. In rare cases, a stubborn infection takes hold which requires a treatment span of 4 to 6 weeks.