[2] When he was young, a "spinal curve" developed which caused significant damage to his nervous system, and would follow him for the rest of his life.

He initially attended common schools of the area, before dropping out of his secondary education after only a single semester due to health issues.

However, after Barnard's resignation in 1860, Allen was offered and accepted positions as an agent for the State Board of Normal Regents and as the director of the teachers' institutes at the university.

Allen, as normal regent board member, reasoned that opening the university to women would help alleviate the issue and fought to departmentalize the existing education classes.

Several students, alumni, and faculty opposed allowing female enrollment, but on March 16, 1863, the normal department opened anyway, with Allen as principal.

[9] Despite its recent founding, the normal department was briefly suspended after the 1863–64 academic year when Allen and 30 of his senior students enlisted in the 40th Wisconsin Infantry Regiment as Hundred Days Men for the still-ongoing Civil War.

Once his health permitted, he started teaching classes in Portland, and helped to open the Bishop Scott Grammar School where he would serve as principal.

On October 22, 1873, he released a report to the Board of Trustees titled "The Objects and Wants of the Normal School", which outlined his philosophy of a liberal education.

The board unanimously adopted the report, and by November the California State Normal School opened a preparatory department, which gave general education to students who otherwise failed their entrance examinations.

The bill was passed by both houses, and the southern branch opened in August 1882 with Allen serving as the nominal principal of the institution for its first year.

[6] In 1892, he was appointed to be a special agent for the California State Board of Horticulture where he made an agricultural survey of Santa Clara County.

[3] In 1893, he supervised a horticultural educational exhibit that was displayed in the California building at the World's Columbian Exposition in Chicago, Illinois.

"[4] Before his death in 1904, alumni who studied under him at the University of Wisconsin wrote that "Prof. Allen was an inspiration to the teachers for careful, conscientious efforts along their line of work.