Conjunctivitis: Bacterial conjunctivitis usually takes 24 to 48 hours to clear but the antibiotic has to be used for 5 to 7 days. Viral conjunctivitis takes longer - 1-2 weeks or longer. Allergic conjunctivitis lasts as long as the allergens are present....Read more.acterial conjunctivitis due to an organism susceptible to vigamox should clear up in a few days. However, viral conjuctivitis, often confused with bacterial conjunctivitis, can take as long as 2 weeks.