We consider two strain influenza model with two vaccination in which strain 2 is the mutation of strain 1. A mutation is a significant change in the genetic makeup that arises due to errors during DNA replication or environmental factors. In this case, strain 2 was assumed to have developed due to alterations in the proteins that comprised strain 1. Proper vaccine administration is a critical component of a successful influenza control program. It is a key part of ensuring that vaccination is as safe and effective as possible. Unfortunately, it is easy to make vaccine administration errors. While certain vaccines administered incorrectly may be valid, such errors can leave patients vulnerable to disease. The aim of this chapter is to study the effect of administering strain 1 (V1) vaccine against strain 2 and strain 2 (V2) vaccine against strain.