The first stop along the line was the County seat, Toms River, established in 1866.  The line was completed to Barnegat in 1879.  The line began primarily as passenger line, but did offer freight service as freight stations were built along the line in the late 1890s.  On January 27, 1893, the Central Railroad of New Jersey bought the line from the Toms River & Waretown Railroad.  Unlike other railbeds that were laid with ballast, the Barnegat Branch was laid with ash from steam locomotives collected at Lakehurst and Red Bank.  Coaling of the locomotives at Barnegat was ceased in March 1920.  (The coaling trestle still stands today.  See below for some pictures of how it looks today.)

Initially, the areas along the line did not populate as fast as the developers would have liked.  For example, Beachwood opened on Memorial Day in 1915, but over the next 10 years only 300 bungalows were built while the town prohibited large hotels.  The town then pursued the feasibility of becoming a retirement community for CNJ employees.  In 1916, the Pennsylvania Railroad made Beachwood a stop on their Philadelphia-Seaside Park-Bay Head line.  However, neither railroad would build a station for their passengers.  As a result, the town of Beachwood constructed their own rail station.  In 1923, New Jersey Pulverizing Company opened a site at Quail Run, just south of Beachwood.

During the depression, some passenger trains kept rolling to Barnegat.  By the early 1930s, the CNJ had replaced all midday trains with Jolly Tar Trail bus service between Lakehurst and Barnegat, leaving "rush hour" and weekend rail service.  (This service was ceased during World War II and the CNJ reverted back to an all-rail schedule.)  A typical passenger train in the mid-1930s consisted of 6 cars.  On Sundays, the CNJ ran a 9 or 10 car "fisherman's train", which was quite popular.  Also, during the depression, the Civilian Conservation Corps worked in reforestation projects.  A Civilian Conservation Corps train departed Barnegat for Reno, Nevada on October 7, 1937 consisting of 10 Pullman and 4 baggage cars.  On April 16, 1939 the NRHS ran an excursion special from Jersey City to Tuckerton.

By 1946, the Barnegat Branch primarily carried summer travelers as the number of regular passengers began to dwindle on the three-hour run between Barnegat and Jersey City.  The CNJ continued its rail service along this line as a show of good will to allow travelers from the southern part of Ocean County to reach the County Seat, which is Toms River.  The CNJ sold the Barnegat station in 1949.  Though passenger service was terminated in the mid 1950s, more industries opened on or near the Barnegat Branch.

Freight deliveries were made three times per week, with the exception of New Jersey Pulverizing at Quail Run, which was daily except Sunday.  In 1952, the Toms River Chemical Company opened with nine buildings and 200 employees and became the branch's largest shipper.  Within twenty years Toms River Chemical Company expanded to thirty buildings and 1,300 employees.  Lacey Materials opened in 1966 near Forked River and brought 40 cars per week.  Though they were not located along the line, they used trucks to ship the material to the Forked River station, where it was then loaded onto the trains.  In December 1964, a siding was built in coordination with the building of Oyster Creek Power Plant.  The siding was only used during construction of the plant and was never used after completion of the plant.  With the exception of deterioration, there were few changes on the branch.  Fairbanks-Mores roadswitchers were slowly removed between 1968 and 1972, thus leaving EMD GP-7s and Alco RS-3s as motive power on the branch.

By 1969, Lacey Materials had ceased shipping and New Jersey Pulverizing turned to trucks.  Toms River Chemical Company was producing anywhere from 7 to 20 cars per day, but there was little traffic south of Toms River.  As a result, the branch was only drilled about twice a week.  In June 1970, the branch was taken out of service between Oyster Creek and Barnegat due the the extremely poor condition of the track.  Jersey Central Power & Light bought a section of the tracks near Oyster Creek from the CNJ, but never used them.  As mentioned on the Main Line page, the Rail Enthusiast special made its way to Toms River on March 1972, and was the last passenger train on the Barnegat Branch.  Many spectators were waiting at the station to see the train arrive.  Aside from the Toms River Chemical Company, the branch only produced  about two per cars per week between Lakehurst and Toms River during 1973.  That same year, tracks were pulled between Oyster Creek and Barnegat.  The Barnegat Branch's future clearly laid in the hands of soon to be created Conrail at this point.