Christ is reminding the disciples of His death and departure (A little while, and ye shall not see me), but He also gives encouragement by telling them that afterwards (and again, a little while) He will be translated to the a different place (with the Father) wherein He will be with them eternally (and ye shall see me).
In this section of John, Jesus is preparing His disciples for His crucifixion and death. He wants them to remain steadfast and hopeful through the trials that come. This is the purpose of the verses that follow:
John 16:19–20 (KJV 1900)
Now Jesus knew that they were desirous to ask him, and said unto them, Do ye inquire among yourselves of that I said, A little while,
and ye shall not see me: and again, a little while, and ye shall see
me? Verily, verily, I say unto you, That ye shall weep and lament, but
the world shall rejoice: and ye shall be sorrowful, but your sorrow
shall be turned into joy