It marks the latest incident as the European Union continues to struggle with the flood of migrants and refugees fleeing conflicts in countries like Syria and Afghanistan or crossing from Africa.
It also coincides with the United Nations' marking International Migrants Day.
Croatian police stopped the van, travelling with British licence plates, near the town of Novska, not far from the Bosnian border.
Inside were almost 70 people, including children.
Many were suffering from carbon monoxide poisoning, and others said they had not eaten nor had anything to drink in days.
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At least 42 were rushed to hospital for treatment.
Dr Maja Grba Buljevic, from the Croatian Institute of Emergency Medicine, says the situation could have been much worse.
"It's very cold, and these people were freezing. Those who were in the most urgent need of care were looked after first, and they've been taken to various hospitals, according to urgency and severity. Thankfully, police on a routine traffic patrol noticed something was wrong with the van. Had they not, the tragedy would've been much greater."
Two Bulgarian nationals have been arrested on suspicion of trying to smuggle the group of people.
Authorities say some people were even inside the van's cargo compartment.
They say the van was headed towards the Croatian capital Zagreb and then on to Western Europe.
It is a route at least 650,000 people travelled across until the pathway was closed in March.
Medicinis Sans Frontieres' Sarah Vuylsteke has told Al Jazeera that has led many migrants and refugees to turn to risky alternatives to try to reach European Union countries.
"What we do know is that, due to the migration policies that the European Union has put in place, the so-called closure of the Balkans routes and keeping people on the islands in Greece and not offering them any safe or legal channels to pass through, (it) is increasingly pushing people to choose more and more dangerous routes, more unsafe routes. And things like this, this is an example of a terrible situation that's being perpetuated by these policies."
In a statement marking International Migrants Day, United Nations secretary-general Ban Ki-moon has praised citizens and communities who have opened their "arms and hearts."
He has called on world authorities to look after migrants regardless of their status and to look at improving migration pathways, both legal and what he calls "irregular."
Golda El-Khoury, from the UN educational, scientific and cultural organisation UNESCO, has suggested many European countries could benefit from migration.
"We know that people, when they move, they find jobs, they integrate into societies. We know, for instance, Europe needs migrants, because these are societies that are ageing and they need many more young people in the workforce. And even before the tragic incidents in the Arab world and the big number of refugees crossing the Mediterranean -- dying in the Mediterranean -- to reach Europe, Europe has systematically received migrants. You know, migration is a global issue. Every country in the world is, in a way, either sending or receiving or a transit country."
Morocco, usually a transit country for people trying to reach Europe, is working to recognise thousands of undocumented migrants within its borders.
Increased security along European borders has meant many are effectively stranded in the North African nation.
Morocco's government recently launched the second phase of a campaign to, as it phrases it, "regularise" migrants' status.
The government is giving them resident permits that allow them to work, enrol their children in school and receive medical care.
The scheme will cover foreigners married to Moroccan nationals who are working or living in the country legally, have lived in the country for five years or have chronic diseases.
Originally from the Philippines, a man named Kyle Santos says he now hopes to get a chance to be recognised in his new home.
"It's very refreshing, because, for me, it's not good to roam around Morocco illegally, and that's why I want to be legal in this place. I love Morocco, I love this place. It's good for the Filipinos, for the immigrants like me. We're very thankful for the King that he gave us amnesty."
