Encephalartos septentrionalis has a wide range, however, it has a fairly small population. Threats at present are unknown, but if threats were identified it seems reasonable that this species could qualify for listing as Vulnerable under criterion C. It was assessed as EN B1+2ab(ii,iii) in Uganda (Kalema and Beentje 2012) but is assessed here as Least Concern across its range as there are no known threats, there are no data on any declines and it is said to be locally common and has a very large EOO.

This species occurs in southern South Sudan (eastern, central and west Equatoria provinces), northern Uganda (Northern region) and in the interior of the Central African Republic (Bamingui-Bangoran, Mbomou and Ouaka prefectures). It is also present in the Democratic Republic of the Congo (Bas-Uele and Haut-Uele provinces). It has been recorded from elevations ranging from 500 to 2,500 m asl.

Despite the fairly wide range, the population size is only estimated to be about 2,000 mature individuals. It is however recorded as being locally common and this population size is likely an underestimate. Available information indicates that the population is stable.

Encephalartos septentrionalis grows in rocky areas in sparse forests and in grassland and open bushland.

The threats to this species are not known, but agricultural activities, increased droughts and poaching by collectors are all potential threats. An unconfirmed report claims that a road being built in an area south of Juba in South Sudan, had destroyed a large number of cycads. This is most likely Encephalartos septentrionalis (Q. Luke pers. comm.).

Poaching by collectors is a potential threat.

This species is listed in Appendix I of the CITES Appendices. Encephalartos septentrionalis occurs in the Imatong Mountain forest reserve in South Sudan and in the Agoru-Agu forest reserve in Uganda. Further west it occurs in the Garamba National Park and in the Bili-Uere Hunting Reserve in the Democratic Republic of the Congo. Plants are possibly present in the Bamingui-Bangoran Conservation Area in the Central African Republic. The level of protection offered in these reserves is unknown. Identification of further suitable sites for the formal protection of this species is needed. An education and awareness programme as well as the long-term monitoring of subpopulations will support the conservation of this species.