Originally, land comprising the present Town of Hannibal was Indian territory. In 1788, the State of New York purchased all the lands of the Onondaga and Oneida Indians except for some small reservations. A good portion of this land became part of the Military Tract which was set aside for the purpose of making land grants to veterans of the Revolutionary War. 

The Military Tract commenced on the southern shore of Lake Ontario at the mouth of the Oswego River, then known as the Onondaga River. The tract included all of current Oswego County west of the river plus the counties of Cayuga, Onondaga, Seneca, Cortland and portions of Wayne, Tompkins and Schuyler Counties. The Military Tract was divided into townships of one-hundred lots of 640 acres each. Robert Harper, then serving as New York's Assistant Secretary of State, was schooled in the classics and drew upon this background when he provided names for the towns in the tract. For instance, Cato was a Roman statesman, Lysander was a Spartan general and of course, Hannibal was a great Carthaginian general. The Military Township of Hannibal included all of the present County of Oswego lying west of the Oswego River, except for 33 lots of the Township of Lysander. In 1791, Hannibal became part of Herkimer County having previously been included in Montgomery County. In 1794, when Onondaga County was formed, the three Military Townships of Hannibal, Lysander and Cicero were placed under the jurisdiction of the Town of Lysander. It is generally believed that the first settler in what is now the Town of Hannibal was Thomas Sprague, Sr., a Revolutionary War veteran who brought his family from Connecticut in 1802 to settle near Bethel. In 1805, other settlers located at Hannibal Center. Among these were Orren Cotton and Watson Earl, who in partnership constructed the first grist mill in the area.

The Military Township of Hannibal was separated from Lysander and made a town by itself within the County of Onondaga on February 28, 1806. The first town meeting for Hannibal was held the first Tuesday of April at the home of Matthew McNair, an innkeeper in the Village of Oswego. William Vaughan was elected the first Supervisor and the first Town Clerk was Edward O'Connor.

The first structure built within the current village limits was a log structure constructed by Henry Jennings in 1808 as a hotel, near what is now the Village Square. Arvin Rice settled near the outskirts of the Village in 1809, constructing himself a log cabin on Oswego Street. After the War of 1812, the Hannibal area was settled more rapidly and developed into a prosperous farming community. In 1815, the first store in the Village of Hannibal was opened by Benjamin Phelps. About the same time, Amos Field from Vermont, built the first frame hotel. On March 1, 1816, the Town of Hannibal and the north 33 lots of Lysander were taken from Onondaga County and made part of the newly created Oswego County. With the annexed 33 lots, the Town of Hannibal then consisted of all of Oswego County lying west of the Oswego River. On April 20, 1818, by act of the New York State Legislature, the Towns of Oswego and Granby were set apart from the Town of Hannibal. The boundaries of the Town of Hannibal have remained fixed ever since and include an area of 27,786 acres. The completion of the Oswego Canal in 1828 stimulated further growth. Hamlets sprung up within the Hannibal Township such as Fairdale, North Hannibal, Hannibal Center, South Hannibal, Kinney's Four Corners and Wiltseville.

By 1835, the population of the Town of Hannibal was up to 2,204 people. It was during this time that the Western Emigration Company was formed in Hannibal for the purpose of establishing a new settlement in the West. As a result, Hannibal residents were directly responsible for the founding of Kenosha, the fifth largest city in Wisconsin. The Village of Hannibal was incorporated on April 7, 1860. The first Village President, Robert M. Rogers, was elected on May 18. The boundaries of the Village, established as a result of a survey done by Alfred B. Worster, enclose an area of 732 acres and 110 rods. At the time, the population of the Village of Hannibal was 416 residents while that of the Township was 3,246.

Several prominent Hannibal residents were involved in the Underground Railroad which assisted the escape of fugitive slaves to Canada. During the Civil War, 1861-65, approximately 400 men, representing the majority of Hannibal's young male adults fought for the Union cause. In 1872, the Lake Ontario Shore Railroad was constructed passing through Hannibal. In the heyday of the railroad, as many as seven passenger trains and 10 to 15 freight trains passed through Hannibal daily. Carloads of dairy products, fruits, bricks, barrels, and cheese boxes produced in Hannibal were shipped to market by rail. Arriving passengers could rent rooms at the American House, now known as the Hannibal Hotel. Disastrous fires in the Village prompted the formation of the Hannibal Volunteer Fire Company in 1910. Eventually, the fire company provided fire protection throughout the Township. Today, it is equipped with the latest state-of-the-art fire fighting equipment. 

From the time of the earliest settlers until World War II, the predominant industry in the Town of Hannibal was farming. Agriculture in the area fostered the growth of related industries and businesses. In the earlier days, farmers and local industries interacted in such a way that the Township tended to be quite self-sufficient. Agricultural pursuits in Hannibal have generally fallen into the three broad categories of dairy farming, vegetable farming and fruit growing. However, there have been exceptions such as the raising of tobacco and poultry farming. Agricultural activities, especially dairy farming, began to decline in the Hannibal area following World War II. However, there are still some significant dairy farms and various fruit farms currently operating throughout the Township. Today, the majority of the Town's working adults have become wage earners in factories and businesses, traveling to Oswego, Fulton, Syracuse and beyond for employment. 

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According to the 1990 census, 613 people live in the Village of Hannibal and 4,616 residents live in the Town of Hannibal. Growth in Fulton, Oswego and Syracuse has stimulated an increase in residential building within the Township.  A modern shopping plaza on Fulton Street in the Village includes the Village Market, a branch office of the Fulton Savings Bank and Eckerd Drugs. The Village Square hosts other businesses such as a video store, Cook’s Manufacturing Jewelers, the Hannibal Quick Mart, C.J.’s Gas & Grill, the Hannibal Hotel and Cam’s NY Pizzeria.  Within the Town of Hannibal are numerous small family owned businesses.  

 In the spring of 1997, a new medical center was opened on Fulton Street.  The same year, natural gas lines were extended into the Village of Hannibal.  Later this year, municipal water will be available to all the residents of the Village of Hannibal and a portion of the Town.  The Hannibal Volunteer Fire Department is in the midst of constructing a major addition to their existing firehouse on Oswego Street.  The Town and the Village of Hannibal are also working together in anticipation of building a new shared municipal building on Cayuga Street to replace the existing overcrowded facility.  Even though the Township remains somewhat a bedroom community, there are definite signs of progress as Hannibal moves forward into the next millennium.