"The stunting rates in Yemen are likely to go up. It means children do not reach their full height but also that their cognitive capacities are affected, which becomes a permanent burden on the whole society," said Anthony Lake in an interview with AFP.
The United Nations has designated Yemen as one of its highest-level humanitarian crises with 80 per cent of the population on the brink of famine.
Aid deliveries have been severely restricted, compounding the crisis from eight months of war that have left 10 million children in need of urgent relief.
"The situation continues to worsen," said Lake. "What we need is a political settlement urgently."
The UNICEF executive director said he was "somewhat" more hopeful than two months ago about prospects for a peace settlement.
Saudi Arabia launched an air campaign in March to push back the Huthi offensive, but the air strikes, which have destroyed a hospital and hit two weddings, have raised alarm.