Mexican police had blocked the migrants from leaving Mexicali for five days. They are hoping to reunite with another group already based in Tijuana.
Many were forced to make the journey on foot given the shortage of lifts on the motorway.
The situation along the border is tense. US President Donald Trump has vowed to prevent migrants from seeking asylum instead choosing to bolster security along the frontier.
Around 3,000 migrants have already arrived in Tijuana. The city's authorities expect that number to reach 10,000 in the coming weeks.
The migrants, mostly fleeing violence and poverty, have been travelling for over a month after the group first formed in San Pedro Sula, Honduras.
