In a letter to the EU's chief Brexit negotiator Michel Barnier, Longfield called for swift guarantees around the residency status of 588,000 children of EU nationals living in England, 260,000 of whom were born in Britain.
Under current EU proposals their future status will only be resolved once details of the jurisdiction of the European Court of Justice (ECJ) are agreed, which is not likely to be until the end of negotiations in 2019.
In the letter to Barnier, Longfield calls for the issue of immigration rights to be separated from ECJ jurisdiction and made a priority.
She warned that refusal to do this risks turning children into "bargaining chips", leaving them in limbo at a time when they are already anxious about their future.
"The EU said they wanted to make residence rights of EU nationals the first thing to be agreed during the negotiations," the letter states.
"Yet their proposal makes residence rights dependent on ECJ jurisdiction, something which won't be agreed until the end of the negotiations.
"If the EU genuinely want to resolve the question of residence rights of EU nationals, they need to separate out the two issues to enable a negotiation in good faith which can give certainty to the hundreds of thousands of children and their families left in limbo. Two more years of uncertainty feels like a long time to a child."
Her letter points out that children who may have to leave the UK after Brexit face considerable disruption to their family life, education and friendships.
The Office of the Children's Commissioner gave the example of one EU family living in the UK where only two of their three children qualified as British citizens due to red tape and administrative hurdles.
In another example, four children of one family from Europe living in the UK all have a different citizenship status.
Longfield has also written separately to Brexit secretary David Davis for clarification on the government's position on the rights of children of EU nationals in the UK.