In 2006, he once again lost his first match at the Medibank International losing to Chris Guccione 6–4, 3–6, 5–7.
At the first slam of the year, the Australian Open, he reached the third round again this time to Nicolas Kiefer 3–6, 2–6, 7–5, 2–6.
He reached his first semifinal of the year at the ATP Buenos Aires losing to compatriot Carlos Moyá 6–3, 6–7, 4–6.
However.
he fell in the first round of the Brasil Open to Flávio Saretta 4–6, 3–6.
At the first two Masters event of the year, the Pacific Life Open and NASDAQ–100 Open, losing to Paradorn Srichaphan 2–6, 2–6 in the third round and Dmitry Tursunov 3–6, 6–7 in the second round, respectively.

He started his French Open preparation at the Open de Tenis Comunidad Valenciana but fell to eventual champion Nicolás Almagro 7–6, 4–6, 4–6.
At the Monte Carlo Masters, he reached the third round, but lost to friend David Ferrer 1–6, 7–6, 3–6.
He reached his second quarterfinal of the year at the Torneo Godó losing once again to Nicolás Almagro 3–6, 3–6.
At the next three events, he lost in the first round of Internazionali BNL d'Italia to Paul-Henri Mathieu 1–6, 3–6 and the third round of the Hamburg Masters to David Ferrer 2–6, 4–6 and of the French Open to Gastón Gaudio 5–7, 5–7, 6–7.
In his Wimbledon preparation, he reached the quarterfinals of the Ordina Open losing to Florent Serra 3–6, 7–6, 3–6.
At Wimbledon, despite leading 2 sets to love against Radek Štěpánek in the third round, he lost in a tight fifth set 7–5, 7–6, 4–6, 2–6, 9–11.

At the Swedish Open reached the quarterfinals, losing to Jarkko Nieminen 6–7, 2–6.
He then fell early at the first round of Croatia Open Umag to Albert Portas and second round of Rogers Cup to Fernando González 2–6, 1–6.
He reached his lone final of the year at the Western & Southern Financial Group Masters, Ferrero notched his first top 10 win of 2006 with a 6–2, 6–4 win over US No.
1 and No.
5 player James Blake.
A few days later, Ferrero defeated No.
2 Rafael Nadal, 7–6, 7–6, and subsequently No.
7 Tommy Robredo, 6–3, 6–4, to move into the final of an ATP Masters Series event for the first time since 2003.
In the final, Ferrero lost to Andy Roddick, 3–6, 4–6.
Ferrero ended the year with a five match losing streak, beginning with the second round of the US Open to Marc Gicquel 5–7, 3–6, 4–6.
This was followed by loses in his first matches at the PTT Thailand Open to Mischa Zverev 6–4, 2–6, 4–6, at the Open de Moselle to Julien Benneteau 4–6, 6–1, 6–7, at the BA–CA–TennisTrophy to Jürgen Melzer 7–5, 6–7, 3–6, and at the Mutua Madrileña Madrid Masters to Robin Söderling 3–6, 2–6.
He ended the year ranked No.
23.
In 2006, he once again lost his first match at the Medibank International losing to Chris Guccione 6–4, 3–6, 5–7. At the first slam of the year, the Australian Open, he reached the third round again this time to Nicolas Kiefer 3–6, 2–6, 7–5, 2–6. He reached his first semifinal of the year at the ATP Buenos Aires losing to compatriot Carlos Moyá 6–3, 6–7, 4–6. However. he fell in the first round of the Brasil Open to Flávio Saretta 4–6, 3–6. At the first two Masters event of the year, the Pacific Life Open and NASDAQ–100 Open, losing to Paradorn Srichaphan 2–6, 2–6 in the third round and Dmitry Tursunov 3–6, 6–7 in the second round, respectively.
He started his French Open preparation at the Open de Tenis Comunidad Valenciana but fell to eventual champion Nicolás Almagro 7–6, 4–6, 4–6. At the Monte Carlo Masters, he reached the third round, but lost to friend David Ferrer 1–6, 7–6, 3–6. He reached his second quarterfinal of the year at the Torneo Godó losing once again to Nicolás Almagro 3–6, 3–6. At the next three events, he lost in the first round of Internazionali BNL d'Italia to Paul-Henri Mathieu 1–6, 3–6 and the third round of the Hamburg Masters to David Ferrer 2–6, 4–6 and of the French Open to Gastón Gaudio 5–7, 5–7, 6–7. In his Wimbledon preparation, he reached the quarterfinals of the Ordina Open losing to Florent Serra 3–6, 7–6, 3–6. At Wimbledon, despite leading 2 sets to love against Radek Štěpánek in the third round, he lost in a tight fifth set 7–5, 7–6, 4–6, 2–6, 9–11.
At the Swedish Open reached the quarterfinals, losing to Jarkko Nieminen 6–7, 2–6. He then fell early at the first round of Croatia Open Umag to Albert Portas and second round of Rogers Cup to Fernando González 2–6, 1–6. He reached his lone final of the year at the Western & Southern Financial Group Masters, Ferrero notched his first top 10 win of 2006 with a 6–2, 6–4 win over US No. 1 and No. 5 player James Blake. A few days later, Ferrero defeated No. 2 Rafael Nadal, 7–6, 7–6, and subsequently No. 7 Tommy Robredo, 6–3, 6–4, to move into the final of an ATP Masters Series event for the first time since 2003. In the final, Ferrero lost to Andy Roddick, 3–6, 4–6. Ferrero ended the year with a five match losing streak, beginning with the second round of the US Open to Marc Gicquel 5–7, 3–6, 4–6. This was followed by loses in his first matches at the PTT Thailand Open to Mischa Zverev 6–4, 2–6, 4–6, at the Open de Moselle to Julien Benneteau 4–6, 6–1, 6–7, at the BA–CA–TennisTrophy to Jürgen Melzer 7–5, 6–7, 3–6, and at the Mutua Madrileña Madrid Masters to Robin Söderling 3–6, 2–6. He ended the year ranked No. 23.
Juan Carlos Ferrero