This question is usually prompted by the biblical teaching of a judgement day for mankind when Christ returns.
More recently the question is also prompted by the commercial success in the USA of the ‘Left Behind’ Christian fiction novels by Tim LaHaye and Jerry B. Jenkins, which present Protestant dispensationalist End Times teachings such as a “pretribulation”, “rapture”, “tribulation” and “premillennial” ordeal. The success of these books also led to films, and even for the authors to produce a series of books targeted at the young adult market, entitled ‘Left Behind: The Kids’.
This answer here doesn’t directly address that second set of concerns about ‘Left Behind’, other than to say that the “rapture”, the disappearance of Christian people, including unbelieving children’s parents, to “heaven”, isn’t scriptural. There are verses such as Matthew 24:31 which do suggest a literal gathering by air:
“Then will appear the sign of the Son of Man in heaven. And then all the peoples of the earth will mourn when they see the Son of Man coming on the clouds of heaven, with power and great glory. And he will send his angels with a loud trumpet call, and they will gather his elect from the four winds, from one end of the heavens to the other.” (Matthew 24:30-31 NIV)
But the context of this and other passages (Matthew 24:40-41, John 19:37/Zechariah 12:10, Acts 1:11, 1 Thessalonians 4:17, Revelation 1:7) speaks of a sudden gathering of some for judgement in Jerusalem, not up to heaven itself – which is never promised in the Bible (cf. John 3:13).
So passing by the ‘Left Behind’ and “rapture” ideas, what does the Bible say will happen to babies and children when Jesus returns?
No mention of children being judged
The first thing to note is that the parable of sheep and goats being separated, and the various other teachings and parables of Jesus concerning judgement are always judgement of individuals for their own actions, not for those of their parents.
On the face of this this contradicts Exodus 34:7 where God “does not leave the guilty unpunished; he punishes the children and their children for the sin of the parents to the third and fourth generation.” However, that verse is generally understood as meaning the consequences of the attitude of Israelite parents to God were to impact those with whom they had living contact, namely as far as grandchildren and maybe even great-grandchildren, but no further. In practice this was the case as one generation worshiping idols in Israel did directly influence the following generations. But as regards individuals God repeatedly stated that was not the way his judgement worked. This is explicit in verses such as the following:
“Yet you ask, ‘Why does the son not share the guilt of his father?’ – Since the son has done what is just and right and has been careful to keep all my decrees, he will surely live.” (Ezekiel 18:19)
So if children of those judged when Christ returns, the children of those immediately seized to Jerusalem and separated into sheep and goats, will not be judged for their parents good or wicked behaviour, then how legitimately can, or would, Christ be in the business of judging children at all?
It is often assumed, particularly by evangelical Christians, that the whole world population would be judged – and non-Christians destroyed – when Christ comes back. But that is not what Christ’s own teaching about his return says. The very idea that the “chosen” will be judged speaks against the idea that millions of people who may have little or no idea about the God of the Bible would be judged. How does the slaughter of most of the earth’s population, guilt only of being clueless, fill the earth “with the knowledge of the glory of the LORD” (Habakkuk 2:14) and similar verses? It doesn’t.
It is difficult to sift out what is literal and what is figurative from the Bible prophecies about the future Kingdom of God on earth, but there is very clear teaching that Christ will be king over a population that is still mortal, still subject to death:
“For He must reign until He has put all His enemies under His feet. The last enemy to be destroyed is death.” (1 Corinthians 15:25-26)
A chance for children to grow up and make up their own minds
The knowledge above that Christ does not come to exterminate the largely non-Christian population of the world, also underlines that babies and children will enjoy health and longevity to may up their own minds.
“Never again will there be in it an infant who lives but a few days, or an old man who does not live out his years; the one who dies at a hundred will be thought a mere child; the one who fails to reach a hundred will be considered accursed. (Isaiah 65:20)
Perhaps that verse from Isaiah is not totally literal in all but guaranteeing that every child will live to 100 at minimum, but it does indicate a significant improvement in health and mortality ages and rates from the moment Christ returns – which is the exact opposite of the random “raptures” in Left Behind fiction (for example in Tim Lahaye’s ‘The Vanishings’ a nurse vanishes as a woman is about to give birth, and the baby disappears before it is born.)
The reassuring news for parents that babies and children have nothing to fear from Christ’s return – in fact the opposite, still leaves hanging the final resolution, that beyond Christ’s return and the immediate judgement for better or worse of “his elect”, as far as the majority of mankind everything does not just continue for ever. The same sentence with promises “For He must reign until He has put all His enemies under His feet. The last enemy to be destroyed is death.” (1 Corinthians 15:25-26) also carries with is the information that Christ’s kingdom, sometimes called ‘the millennium’ since it is portrayed as having “a thousand years” in Revelation, is in fact only a transitional period between the return of Christ and the final end of mortality. As Paul presents it in 1 Corinthians 15 it is a kind of interregnum between Christ’s reign and his Father’s ultimate reign.
This gives rise to other questions: Are Revelation’s “thousand years” literally 12,000 calendar months, or just some unimaginably long period enabling the generation just born at Christ’s return to live out the maximum lifespan of which a human body is capable in ideal conditions? Or what about new babies in the kingdom? Presumably at some point human reproduction must stop, or there will always be a generation which are just infants when Christ finally hands the kingdom upward to his Father??
We don’t have the answers to these questions, and right now we don’t need them. We do have the answer to the question asked. “What will happen to babies and children when Jesus returns?” – They are not all going to be destroyed with the earth’s population in some great cataclysm; also they are not going to be raptured to heaven or left behind based on their parents church affiliation; instead they will have a wonderful opportunity to grow up a world with Christ as their global president. And then at the end of that we reach the end of the end, as Paul had said earlier, when even death itself will be conquered:
“He will wipe every tear from their eyes. There will be no more death’ or mourning or crying or pain, for the old order of things has passed away.” (Revelation 21:4)