[7] On 15 December 2016, the Supreme Electoral Tribunal decided, by two votes to one, to allow Hernández to stand in the primary elections by the National Party of Honduras on 12 March 2017.

Hernández said National Party accountants found that approximately L3 million lempira (about US$140,000) from companies with links to the Honduran Social Security Institute (IHSS) scandal had entered its campaign coffers.

According to the United Nations and the Inter-American Commission on Human Rights, "many of them were transferred to military installations, where they were brutally beaten, insulted and sometimes tortured".

[33][34][35][36] In May 2015, Radio Globo discovered documents that allegedly showed that the Honduran National Party had received large amounts of cash from nonexistent companies through fraudulent contracts awarded by the IHSS when it was run by Mario Zelaya.

[38] On 21 June 2018, president Hernández ordered units of the Honduran Army and the military police in the streets of the capital after renewed protests.

[39] In April 2019, new anti-privatisation and anti-corruption protests erupted, led by Tegucigalpa Autonomous University students and by health care workers.

President Hernández criticized his brother's conviction as basado en testimonios de asesinos ("based on testimony from killers") and denied that Honduras has become a narco-state.

[48][49] The social manager of the official Facebook pages of both Hernández and his late sister, who had served as communications minister, was directly controlling several hundreds of these fake entities.

[48] This campaign innovated by using Facebook's Organization Pages, configured with human names and photos, to add apparent support and to lure unaware readers.

[50] In 2019, during the Venezuelan presidential crisis, Hernández recognized the legitimacy of Juan Guaidó as president of Venezuela and joined the declarations of the Lima Group, against the Maduro government.

[52] Shortly before leaving office, in October 2021, contrary to his alliance with the US, Hernández met Nicaragua's Ortega in Managua, where they signed agreements regarding disputes in the Caribbean Sea and the Gulf of Fonseca, on which there had been a ruling by a The Hague court years earlier.

The summit between Hernández and Ortega was described as "strange", "surprising", and "unusual" by El País, given the leaders' differences in previous years.

[53] At the end of May 2019, U.S. prosecutors unsealed documents from 2015 which revealed that Hernández was himself the subject of a major drug trafficking and money laundering investigation, alongside his sister Hilda and others.

[54][55] Hernández was identified as a co-conspirator in a drug trafficking and money laundering case against his brother, according to document filed in U.S. district court.

Tony Hernández was sentenced to life in prison in January 2021 following his conviction on numerous charges related to his work in drug trafficking.

On 14 February, he was surrounded by the National police and DEA agents at his residency to process his capture and eventually take him to custody of the United States for possible trials.

[64] The United States specifically charged Hernández with accepting millions of dollars in bribes from narcotraffickers since 2004, and in particular the Sinaloa Cartel, led at the time by Joaquín "El Chapo" Guzmán, since 2012.