The hamlet of Port Republic, Virginia, lies on a neck of land between the North and South Rivers, which conjoin to form the South Fork Shenandoah River. On June 6–7, 1862, Jackson's army, numbering about 16,000, bivouacked north of Port Republic, Maj. Gen. Richard S. Ewell's division along the banks of Mill Creek near Goods Mill, and Brig. Gen. Charles S. Winder's division on the north bank of North River near the bridge. The 15th Alabama Infantry regiment was left to block the roads at Union Church. Jackson's headquarters were in Madison Hall at Port Republic. The army trains were parked nearby.

Two Union columns converged on Jackson's position. The army of Maj. Gen. John C. Frémont, about 15,000 strong, moved south on the Valley Pike and reached the vicinity of Harrisonburg on June 6. The division of Brig. Gen. James Shields, about 10,000, advanced south from Front Royal in the Luray (Page) Valley, but was badly strung out because of the muddy Luray Road. At Port Republic, Jackson possessed the last intact bridge on the North River and the fords on the South River by which Frémont and Shields could unite. Jackson determined to check Frémont's advance at Mill Creek, while meeting Shields on the east bank of the South Fork of the Shenandoah River. A Confederate signal station on Massanutten monitored Union progress. The Confederate forces (5,800-strong) under John C. Frémont successfully defended their position and repulsed the attack of the Union forces (11,500-strong) under Richard S. Ewell, forcing Frémont to retreat with his forces.