In the fall of 1803, the Lewis and Clark Expedition set out from St. Louis, Missouri, which was then a town on the American frontier. On May 14, 1804, the expedition's boats started their path up the Missouri River. Heading upstream, travel progressed extremely slowly.

One of the initial problems faced by the expedition was its lack of a translator to communicate with the Native Americans in the area. On September 25, 1804, the expedition became embroiled in a conflict with a group of Sioux Indians in South Dakota. A few shots were fired, but fortunately no serious violence erupted. However, Lewis and Clark realized they had a long way to go and many had many more Indian tribes to face. They knew they needed an interpreter to help steer them out of future problems. On October 27, 1804, the expedition reached a Mandan village in North Dakota, marking their entry into what was now mostly unexplored, unmapped territory. The Mandans and the Hidatsas displayed a friendly, and even curious, attitude toward the white men. Since the temperatures in this region could often plummet to well below zero, the expedition decided to set up camp at the village for the winter, rather than travel further in the harsh weather. They referred to their camp as Fort Mandan.

The expedition received some visitors while at the Mandan village, and one of these was Toussaint Charbonneau, Sacajawea's husband. Charbonneau, able to communicate by sign language with most of the region's Native Americans, offered his services as an interpreter. He seemed to be just what Lewis and Clark were looking for, so they hired him during his visit, on November 3. However, it soon became clear that the trapper's wife might also prove a great boon to the explorers: she brought warm buffalo robes to the freezing men, instantly endearing herself to the officers; and after this act of generosity, Lewis and Clark decided to let Charbonneau bring his "squaw" along on the trip.

When she joined the Lewis and Clark Expedition, Sacajawea was only sixteen, but was already several months into a pregnancy. During the winter at Fort Mandan, she went through a particularly painful labor, with only a traditional remedy, the powder of a snake's rattle, to ease her pain. In February of 1805 she gave birth to a boy. Sacajawea and Charbonneau named the child Jean Baptiste, although the Lewis and Clark Expedition members would universally refer to him by the nickname "Pomp". "Pomp" meant "first-born" in the Shoshoni language. In the spring of 1805, the expedition set out to continue up the Missouri River, and Pomp went with them. Remarkably, during the first two years of his life, Pomp would never leave the Lewis and Clark Expedition; he would ride thousands of miles on his mother's back.

The purpose of the Lewis and Clark Expedition was to explore the Louisiana Territory. President Jefferson's ambassadors had negotiated the purchase of this vast property from Napoleon in 1803, and Jefferson sent Lewis and Clark to explore the unknown parts of the territory and bring back a report. The main goal of the mission was to explore the Missouri River and its tributaries, in hopes of finding a good water route for reaching California and the Pacific Ocean. Jefferson chose to send his former secretary, Captain Meriwether Lewis, to lead the expedition. Lewis insisted on sharing command with Captain William Clark. The pair kept detailed journals of their mission (they even brought along writing desks to work at during the trip, but these were soon destroyed due to the rigors of the trail). Jefferson encouraged the other men on the expedition to keep journals as well, and the few who could read and write followed the President's bidding. As a result, the expedition received extraordinarily good documentation, providing multiple accounts of important events. Among other things, these journals serve as the major record of Sacajawea's life. Clark's journal was probably the most complete report regarding Sacajawea, as he was very fond of her and her son; most of what is known regarding Sacajawea is derived from Clark's journal. Everyone involved knew the expedition would prove extremely difficult, and Lewis and Clark received only 2500 dollars from the U.S. government to furnish supplies. The dollar was worth much more then, but the amount still seemed insufficient to finance such a long and dangerous journey. The supplies the explorers brought contained presents to give to Native Americans they came into contact with along the way. Although hoping to avoid violence, the expedition also brought a large amount of weaponry, and even brought a gun specialist to repair guns. (The men ended up relying on guns much more for hunting than for fighting.) The expedition included a diverse group, including French-Canadians like Charbonneau, Clark's African-American servant York, and, of course, Sacajawea, a Shoshoni. Sacajawea was the only female member of the expedition. Charbonneau, at 46, was the oldest.

Sacajawea, who would become one of the most important members of the Lewis and Clark Expedition, was never actually hired. Instead, Lewis and Clark allowed her to come along when they hired her husband. The explorers never expected her to play the crucial role she would, although there is some indication that Clark thought very early that she would be good person to have along when it came to negotiating with the Shoshoni for horses. Sacajawea contributed more to the expedition than just her knowledge of the region and her positive attitude. As a Native American woman carrying a baby, she also was a sign to various Native American groups that the approaching group of white men did not mean to make war. Everyone knew that men anticipating outbreaks of violence would not bring along a woman with a baby on her back. This probably saved the expedition more than once.

From the start, Sacajawea found the expedition intriguing. She loved to quietly observe the men in their European customs, for example during the Christmas party they threw while at Fort Mandan. Having lived a rough life as a captive of the Hidatsa, Sacajawea was looking forward to the expedition; she knew the expedition would pass through Shoshoni territory, and she hoped it would bring her into contact with the tribe she had been stolen from.