What does John 16:16 mean?

This is part of Jesus' final instructions to His closest disciples, on the night of His arrest (John 13:1–5; 18:1–3). Jesus has predicted His absence several times (John 14:3–4; 16:5). This is consistent with His earlier explanations that the Messiah was sent, in part, as a sacrifice (Mark 8:31). However, the disciples don't fully understand (John 16:17–18). Much of that confusion is because they don't have the benefit of hindsight—they have not yet witnessed everything that is about to happen (John 2:22). It's also because they don't yet have the influence of the Holy Spirit, who will help them grasp these things (John 16:13).

This remark is another which stumps the disciples. Since Christ has spoken very recently about leaving, that aspect is less obscure. What seems to confuse these men most is the idea that after some time, they will again see Christ. Most likely, Jesus is referring to the time between His resurrection (John 20:19) and His ascension (Acts 1:6–9). During that 40-day period (Acts 1:3), He will once again be visible and present with the disciples on earth.