Bulbophyllum vakonae is endemic to Madagascar and is known from 42 collections representing 21 occurrences. Twenty-three collections (10 occurrences) have been recorded in six protected areas, the Marojejy-Anjanaharibe Sud-Tsaratanana Corridor (COMATSA) (two occurrences, one location), the Analamazaotra National Park (two occurrences, one location), the Mantadia National Park (one occurrence, one location), the Protected harmonious landscape of the Anjozorobe-Angavo complex (one occurrence, one location), the Vohibe forest - Ankeniheny-Zahamena Corridor (two occurrences, one location) and the Torotorofotsy Protected Area (two occurrences, one location). In addition to these officially protected sites, 14 collections (six occurrences) of this species have also been made on the footprint of a mining project undergoing intense human pressure such as forest clearing. These former occurrences were collected on individuals that must be considered as extirpated. Two collections (two occurrences) of this species have been made in the conservation zone surrounding the footprint of the mining project. This conservation zone should be subjected to protection in the near future. It is also known from three collections (three occurrences, three locations) made from Andramalana, Andomotra, and Maharavana in unprotected forest subjected to selective logging, timber harvesting for small-scale subsistence, slash-and-burn agricultural practices (Tavy), and fire for grazing. The species is thus known from 42 collections representing 15 existing and six extirpated occurrences.

The extent of occurrence (EOO) of Bulbophyllum vakonae is estimated to be 48,632 km² (largely exceeding the limits for Vulnerable status under criterion B1) and its minimal area of occupancy (AOO) is estimated to be 52 km² (which falls within the limits for Endangered status under the criterion B2). These 15 remaining occurrences represent a total of 10 locations (sensu IUCN 2019) with respect to the main threat, selective logging, timber harvesting. The loss of the subpopulation in the footprint of a mining project and inferred extirpated occurrences by fire for grazing have induced a continuous decline of the EOO, the AOO, the number of subpopulations, locations, and the number of mature individuals. Bulbophyllum vakonae is therefore assigned a status of VU B2ab (i,ii,iii,iv,v).

Bulbophyllum vakonae is endemic to Madagascar where it occurs in the former provinces of Antsiranana in the Sava Region (Andramanalana, Andranomilolo), of Antananarivo in the Analamanga Region (Andomotra, Anjozorobe), of Fianarantsoa in the Haute-Matsiatra, Amoron'i Mania Regions (Ambalavao, Maharavana) and of Toamasina in the Alaotra-Mangoro, Atsinanana Regions (Analamazaotra, Mantadia, Ampitambe-Moramanga, Vohibe, Torotorofotsy). The species is known from the eastern escarpment forest or/and from the high Plateau on inselbergs.

The population of Bulbophyllum vakonae is currently thought to be decreasing since the species habitat is threatened by forest clearing due to mining activities, and forest degradation by selective logging, timber harvesting for small-scale subsistence, fire for grazing, and slash-and-burn practices (tavy). The number of mature individuals of B. vakonae is not known and cannot be estimated since the species is an epiphyte on the trunk, on branches in the canopy, or a lithophytic species exposed to sunny places.

Bulbophyllum vakonae is an epiphytic herb growing on the trunk, on branches in the canopy on moss and lichen-covered trees. Also, a lithophytic species exposed to sunny places in humid and subhumid forests, inselberg/rock faces at elevations of 538 to 1,644 m asl (Madagascar Catalogue 2020).

This species is threatened by selective logging, timber harvesting for small-scale subsistence, and slash-and-burn agricultural practices (tavy). Six occurrences of this species have been collected on the footprint of a mining project undergoing intense human pressure such as forests clearing. It is also known from three occurrences in unprotected forests subject to selective logging, timber harvesting for small-scale subsistence, slash-and-burn agricultural practices (Tavy), and fire for grazing.

There are no reported uses of this species, but it may be sought after by specialist collectors.

Bulbophyllum vakonae has been recorded from five protected areas, Marojejy-Anjanaharibe Sud-Tsaratanana Corridor (COMATSA) (two occurrences), Analamazaotra National Park (two occurrences), Mantadia National Park (one occurrence), Protected harmonious landscape of the Anjozorobe-Angavo complex (one occurrence), Torotorofotsy Protected Area (two occurrences) and Vohibe forest - Ankeniheny-Zahamena Corridor (two occurrences). Four collection (four occurrences) of this species have also been made in the conservation zone surrounding the footprint of a mining project undergoing intense human pressure such as forests clearing. This conservation zone should be subjected to protection in the near future. The species is included in Appendix II of CITES. Several individuals of this species have been brought to cultivation in the Antananarivo and the Ambatovy shade houses. Ex situ conservation is recommended (micro-propagation, seed banking). Further awareness building is recommended for local communities and national authorities.