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Megiddo was his first objective as it was a key logistical point and had to be taken, at all costs. When he reached Aaruna, Thutmose III took counsel with his generals. There were two routes to Megiddo, a long, easy and level road around the hills, which the enemy expected Thutmose III to take, and a route which was narrow, difficult and cut through the hills.

His generals advised him to take the easy road through the hills. However, Thutmose disagreed, citing surprise as a powerful advantage to be sought, and through rousing speaches he motivated his men to follow him through the hills. Thutmose personally led his men on foot through the hills, with the journey taking about twelve hours for the vanguard to reach the valley on the other side and another seven hours before the last troops emerged.

Thutmose himself waited at the head of the pass till the last man was safely through. The sudden and unexpected appearance of Egyptians in their rear forced the coallition forces to make a hasty re-deployment of their troops. There are said to have been over 300 allied kings, each with his own army, which would have been am immense force at that time.

However, Thutmose was determined, and when the coallition saw him at the head of his men, leading them forward, they lost their resolve and fled for the city of Megiddo. The Egyptian army, being young and inexperienced, took to looting and lost the opportunity of taking the city immediately. Thutmose was disappointed and so settled for a siege of Megiddo.

A moat was dug around the city walls and this was finished off with a strong wooden palisade. The king gave orders to let nobody through except those who signalled at the gate that they wished to surrender.