Emigrant Wilderness Historical Use Preservation Act - (Sec. 3) Requires the Secretary of Agriculture (USDA) to ensure that all pack and saddle stock uses within the Emigrant Wilderness of Stanislaus National Forest in California are recognized as appropriate wilderness activities, including the effect on soil, water, and vegetation. Prohibits any action from being taken to limit or exclude pack and saddle stock without an environmental analysis with a finding that the actions are necessary to preserve the wilderness character of the area to that which existed at the time of the designation.

States that historical uses and activities, including commercial outfitting and guiding, camping, pack stock grazing; and associated campfires, tent locations, and social trails are traditional uses. Requires signs of use created by these activities to be considered substantially unnoticeable and acceptable as long as they do not exceed the level present at the time of the designation. Requires the USDA to take actions to ensure that these levels are not exceeded.

Direct the USDA to complete an updated wilderness plan to preserve pack and saddle stock use and all legally acceptable recreational uses within the area. Specifies requirements for the plan.

Requires the USDA to continue to authorize commercial pack and saddle stock services and issue authorizations to provide commercial services for commercial stock operations within the area at historic levels. Requires the USDA to specify levels of use, user days, and activities by commercial outfitters and guides.

Emigrant Wilderness Historical Use Preservation Act of 2013 - Declares that this Act modifies and supplements federal law applicable to the Emigrant Wilderness of the Stanislaus National Forest in California.

Directs the Secretary of Agriculture (USDA) to ensure that, within the Emigrant Wilderness, the level of use, allotted user days, and activities by commercial outfitters and guides shall not rise above or be restricted below the historical level of use, allotted user days, and activities by commercial outfitters and guides within that area that existed as of the original designation of the Wilderness on January 3, 1975.

Prohibits any increase or reduction in the level of commercial pack and saddle stock use from the highest level of such use in the preceding 10 years.

Allows the historical use of trails, roads, paths, campsites, meadows, and cross-country areas in the Wilderness by recreational and commercial pack and saddle stock to continue.

States that the use of drift fences that are in existence or were previously in existence at the time of the Wilderness' designation shall be allowed and maintained.